Methods of treating autophagy-associated disorders and related pharmaceutical compositions, diagnostics, screening techniques and kits

ABSTRACT

The invention provides methods of treating autophagy mediated diseases and disorders and related pharmaceutical compositions, diagnostics, screening techniques and kits. In one embodiment, the invention provides a method of determining whether a subject suffers from, or is at risk of developing, and autophagy mediated disease state and/or condition by evaluating LC3 levels.

RELATED APPLICATIONS

This application is a continuation application of U.S. patentapplication Ser. No. 14/116,581, filed Nov. 8, 2013 of identical titlewhich claims priority to International Patent Application No.PCT/US2012/037300 filed May 10, 2012, which itself claims priority fromU.S. Provisional Application Ser. No. 61/484,653 filed May 10, 2011,entitled “Autophagy Diagnostics, Screening, and Therapeutics”, thecomplete disclosure of each of said applications is hereby incorporatedby reference in its entirety.

GOVERNMENT SUPPORT

The invention described herein was funded in part by National Instituteof Health Grant No. R01 A1069345. Accordingly, the United States hascertain rights in the invention.

FIELD OF THE INVENTION

The invention provides methods of treating autophagy-associateddisorders, and related pharmaceutical compositions, diagnostics,screening techniques and kits.

BACKGROUND OF THE INVENTION

Autophagy is a homeostatic process highly conserved in eukaryotic cellswhere it acts as a cytoplasmic biomass quantity and quality controlsystem (Mizushima et al., 2008; Yang and Klionsky, 2010). Its functionsencompass programmed cell survival and cell death, normally skewedtoward cell survival (Kroemer and Levine, 2008) through provision ofenergy and nutrients and ridding the cytoplasm of toxic macromolecularaggregates, faulty organelles (Mizushima et al., 2008; Yang andKlionsky, 2010) and invading microorganisms (Deretic and Levine, 2009;Levine et al., 2011).

The cell-autonomous antimicrobial defense functions of autophagy,demonstrated initially in the case of streptococci (Nakagawa et al.,2004) and Mycobacterium tuberculosis (Gutierrez et al., 2004; Harris etal., 2007; Ponpuak et al., 2010), have been extended to a wide varietyof microbes with a caveat that most highly adapted pathogens haveevolved specific protective mechanisms against autophagic elimination ofmicrobes (Deretic and Levine, 2009; Gannage et al., 2009; Kyei et al.,2009; Lee et al., 2009; Orvedahl et al., 2007; Yoshikawa et al., 2009).Other studies have uncovered orderly intersections between autophagy andinnate (Chaturvedi et al., 2008; Cooney et al., 2010; Delgado et al.,2008; Huang et al., 2009; Sanjuan et al., 2007; Shi and Kehrl, 2010;Tang et al., 2010; Travassos et al., 2009; Xu et al., 2007; Yano et al.,2008) and adaptive immunity (Blanchet et al., 2010; Lee et al., 2010;Munz, 2009; Nedjic et al., 2008; Paludan et al., 2005), T celldevelopment, differentiation and homeostasis (Jia and He, 2011; Nedjicet al., 2008), and inflammatory responses (Cadwell et al., 2010; Jounaiet al., 2007; Levine et al., 2011; Saitoh and Akira, 2010). Autophagysuppresses endogenous, cell-autonomous promoters of inflammation (Mathewet al., 2009; Orvedahl et al., 2010).

Specific autophagic factors, such as Atg5-Atg12, have been shown toinhibit RIG-I signaling (Jounai et al., 2007) whereas Atg9, have beenreported to negatively regulate trafficking, assembly and activation ofTBK-1 (TANK-binding kinase 1), which, among its key functions, controlstype I interferon response elicited by intracellular double stranded DNA(Saitoh et al., 2009). In the context of anti-inflammatory function,recent studies indicate that autophagy plays an inhibitory role ininflammasome and IL-1p activation by mechanisms that involvemitochondrial homeostasis (Nakahira et al., 2010; Zhou et al., 2011) orpotentially direct effects (Harris et al., 2011): Finally, a number ofgenetic links have been found in human populations between autophagy andidiopathic inflammatory (Consortium, 2007; Craddock et al., 2010) orinfectious diseases such as tuberculosis (Che et al., 2010; Intemann etal., 2009; Singh et al., 2006; Singh et al., 2010), with significantinflammatory components and tissue damage.

Given the interconnectedness of autophagy and immunity, it is likelythat the immune manifestations of autophagy are affected not only by theinduction of autophagy but also by the completion of the autophagicpathway. The formation of the autophagic organelles of the sensu strictoautophagy pathway (also referred to as macroautophagy) depends onmultiple sources of membrane or regulatory factors (Tooze and Yoshimori,2010). The key stages of autophagy however are not restricted to theformation of autophagosomal membranes and include the sequestration ofthe earmarked cargo by the autophagic adaptors (Bjorkoy et al., 2005;Kirkin et al., 2009; Thurston et al., 2009; Wild et al., 2011), and theless understood process of the maturation of autophagic organelles intoautolysosomes where the captured material is degraded (Korolchuk et al.,2011; Liang et al., 2008; Matsunaga et al., 2009; Zhong et al., 2009).

Thus, autophagy is directly implicated in cancer, type II diabetes,neurodegenerative syndromes such as Alzheimer's, Huntington's andParkinson's diseases, chronic inflammatory diseases (e.g. Crohn'sdisease), type II diabetes, infections (such as tuberculosis and HIV (Iand II)/AIDS, hepatitis B, hepatitis C), and a variety of disordersassociated with aging. A better understanding of how autophagicmechanisms are implicated in the aforementioned diseases could provecritical to preventing or treating these maladies.

The references which are cited above are presented after Example 2 ofthe present specification.

SUMMARY OF THE INVENTION

The elucidation of certain autophagic processes involved in the onsetand progression of a variety of infectious and inflammatory-relateddisorders has led to the discovery of methods of treating and diagnosingsuch ailments. Further, the discovered novel methods have led to ourbeing able to identify compounds that are effective as modulators ofautophagy in the treatment of infectious and inflammatory-relateddisorders, as well as versatile techniques that enable the highthrough-put analyses of autophagic processes, including the diseasestate in a patient for diagnosis and/or monitoring therapy of thedisease state. The present invention is directed to a method ofidentifying compounds which exhibit biological activity as modulators(inhibitors or agonists) of autophagy and consequently, can be used inthe treatment of diseases which occur or are mediated through autophagyas a mechanism.

In one embodiment, the present invention provides a method of modulatingautophagy in a biological system, in particular a patient or subject. Inthis aspect of the invention, a compound identified herein as anautophagy modulator (inhibitor or agonist, also referred to genericallyas an “autostatin”) is presented to the biological system, includingadministration to a patient or subject in need, in order to modulate(often enhance or up-regulate but in certain instances, for examplecancer, inhibit) autophagy and effect a favorable result in thebiological system, often a patient or subject. The resulting modulationmay be monitored or applied in the biological system to effect afavorable result, including the inhibition, treatment and/or preventionof cancer, including metastasis of cancer, or the inhibition, treatment(including the amerlioration of symptoms) and/or prevention of one ormore disease states or conditions in which the modulation, especiallyincluding upregulation or inhibition of autophagy provides a favorableresult in numerous disease states and/or conditions includingneurodegeneration (including, for example, Alzheimer's disease,Parkinson's disease; other ataxias), chronic inflammatory diseases(including, for example, inflammatory bowel disease, including Crohn'sdisease, rheumatoid arthritis, lupus, multiple sclerosis, chronicobstructive pulmony disease/COPD, pulmonary fibrosis, cystic fibrosis,Sjogren's disease), diabetes and metabolic syndrome, muscle degenerationand atrophy, frailty in aging, stroke and spinal cord injury,arteriosclerosis, infectious diseases (HIV I and II, HBV, HCV, includingsecondary disease states or conditions associated with infectiousdiseases, including AIDS) and tuberculosis, among others. The commonprinciple of this embodiment of the invention is that compounds,including autostatins which are autophagy modulators (i.e., inhibitorsor activators of autophagy), depending upon the disease state, conditionor symptom to be treated, may cure, prevent (including reducing thelikelihood of), improve prognosis, ameliorate symptoms and/or improvethe quality of the patient's or subject's life. In addition, in thetherapeutic aspects of the invention, the administration of an autophagymodulator (autostatin) may prolong the life of the patient, as well asimprove the quality of life in the aging patient or subject.

In one embodiment the method of treating an autophagy-mediated diseasestate or condition comprising administering at least one autostatinalone or optionally in combination with at least one additionalbioactive agent. In this method an autostatin selected from the groupconsisting of flubendazole, hexachlorophene, propidium iodide, bepridil,clomiphene citrate (Z,E), GBR 12909, propafenone, metixene, dipivefrin,fluvoxamine, dicyclomine, dimethisoquin, ticlopidine, memantine,bromhexine, norcyclobenzaprine, diperodon and nortriptyline,tetrachlorisophthalonitrile and phenylmercuric acetate, pharmaceuticallyacceptable salts thereof and mixtures thereof, alone or in combinationwith at least one additional bioactive agent, optionally in combinationwith a pharmaceutically acceptable carrier, additive or excipient, maybe administered to a patient or subject in need to treat anautophagy-mediated disease state and/or condition. It is noted thatflubendazole, hexachlorophene, propidium iodide, bepridil, clomiphenecitrate (Z,E), GBR 12909, propafenone, metixene, dipivefrin,fluvoxamine, dicyclomine, dimethisoquin, ticlopidine, memantine,bromhexine, norcyclobenzaprine, diperodon, nortriptyline and theirpharmaceutically acceptable salts show activity as agonists or inducersof autophagy in the treatment of an autophagy-mediated disease,tetrachlorisophthalonitrile, phenylmercuric acetate and theirpharmaceutically acceptable salts, find use as antagonists or inhibitorsof autophagy. All of these compounds will find use as modulators ofautophagy in the various autophagy-mediated disease states andconditions described herein, with the agonists being preferred in mostdisease states other than cancer and in the case of the treatment ofcancer, the inhibitors described above are preferred, alone or incombination with an autophagy agonist as described above and/or anadditional anticancer agent as otherwise described herein.

Pharmaceutical compositions according to the present invention comprisean effective amount of at least one autophagy modulator selected fromthe group consisting of flubendazole, hexachlorophene, propidium iodide,bepridil, clomiphene citrate (Z,E), GBR 12909, propafenone, metixene,dipivefrin, fluvoxamirie, dicyclomine, dimethisoquin, ticlopidine,memantine, bromhexine, norcyclobenzaprine, diperodon, nortriptyline,tetrachlorisophthalonitrile, phenylmercuric acetate and theirpharmaceutically acceptable salts, optionally in combination with apharmaceutically acceptable carrier, additive and/or excipient andfurther optionally, in combination with at least one additionalbioactive agent (e.g., an anticancer agent, antibiotic,anti-tuberculosis agent, antiviral agent such as an anti-HIV agent,anti-HBV agent or anti-HCV agent, etc.), preferably at least oneanticancer agent as otherwise disclosed herein or at least oneadditional autophagy modulator as otherwise described herein. In thepresent invention, an additional autophagy modulator (autostatin) isselected from the group consisting of may be combined with an additionalautophagy modulator selected from the group consisting of benzethonium,niclosamide, monensin, bromperidol, levobunolol, dehydroisoandosterone3-acetate, sertraline, tamoxifen, reserpine, hexachlorophene,dipyridamole, harmaline, prazosin, lidoflazine, thiethylperazine,dextromethorphan, desipramine, mebendazole, canrenone, chlorprothixene,maprotiline, homochlorcyclizine, loperamide, nicardipine,dexfenfluramine, nilvadipine, dosulepin, biperiden, denatonium,etomidate, toremifene, tomoxetine, clorgyline, zotepine, beta-escin,tridihexethyl, ceftazidime, methoxy-6-harmalan, melengestrol,albendazole, rimantadine, chlorpromazine, pergolide, cloperastine,prednicarbate, haloperidol, clotrimazole, nitrofural, iopanoic acid,naftopidil, methimazole, trimeprazine, ethoxyquin, clocortolone,doxycycline, pirlindole mesylate, doxazosin, deptropine, nocodazole,scopolamine, oxybenzone, halcinonide, oxybutynin, miconazole,clomipramine, cyproheptadine, doxepin, dyclonine, salbutamol, flavoxate,amoxapine, fenofibrate, pimethixene and mixtures thereof.

In an additional embodiment, the invention provides a method ofmonitoring or determining whether a subject is responding to therapywith an autophagy modulator (autostatin) suffers from, or is at risk ofdeveloping a disease or condition which is an autophagy-mediated diseaseor condition, the method comprising measuring LC3 levels in a bloodsample of the patient or subject, measuring the LC3 levels in saidsample and comparing the LC3 levels with a control, wherein ameasurement of LC3 levels in said sample which is higher or lower thanthe control (the control may be derived from a sample of tissue fromhealthy, disease-free individuals or individuals known to have a diseasestate or condition being identified) is evidence of the likelihood ofthe existence of said disease state or condition in said tissue of saidpatient. It unexpectedly has been discovered that LC3 polypeptide isexpressed on blood cells, in particular, mononuclear cells Thisdiscovery makes analysis readily amenable to immunohistochemistry,immunostaining, immunofluorescence and western blot assay. Also, themethod can use monoclonal or polyclonal antibodies. In one embodiment,the assay is a sandwich assay for point of care or home use.

In another embodiment, the present disclosure provides a clinicallyusable assay that can be applied for diagnostics and monitoring theprogression of therapy of an autophagy mediated disease using an easy toobtain blood sample from a patient or subject. It is based upon theunexpected discovery that LC3 polypeptides are expressed on the surfaceof blood cells, in particular, peripheral blood mononuclear cells (PBMC)in particular, primary lymphocytes. Counterintuitively, given theengagement of autophagy and intracellular membranes, the expectation isthat LC3 polypeptides are found exclusively intracellularly, yet, it hasbeen discovered by the present inventor that LC3 as an an autophagymarker can be detected on the surface of cells, in particular primarylumphocytes. The inventors find surprisingly that LC3 polypeptide (whichhas heretofore been found only on intracellular membranes detectable bycomplicated methods of microscopy) is detected by simple antibodystaining on the cell surface of primary lymphocytes using antibodies andflow cytometry or other simple assays of detection, including antibodyassays such as an ELISA assay. This makes the quantification of LC3 inblood/plasma samples of patients relatively facile. This information(i.e., the relative level of LC3 expressed in the blood of a patient) isuseful for diagnosis, prognosis and monitoring of the effective oftherapy of disease states and/or conditions which are mediated throughauthophagy.

Based on prior art understanding regarding autophagy, one could notpredict that LC3 polypeptide, including LC3B, would be exposed on thesurface of the plasma membrane of the cell, such as a blood lymphocyteand be amenable to identification with surface based assays, includingantibody-based assays or flow cytometry. This is due to the acceptedtopology of the LC3 distribution on the intracellular membranes.According to prior art convention, even if the intracellular membraneswere to fuse with the plasma membrane (PM), LC3 would not be exposed tothe outside (the surface of the cell); according to conventionalunderstanding, LC3 would always be shielded from the exposure to theoutside and not accessible to antibodies, unless the cells werepermeabilized). In one embodiment, in the present invention, it has beendiscovered unexpectedly that LC3 is exposed on the external cell surface(i.e., on the external side of the plasma membrane facing the outside ofthe cell, rather than the inside surface) and thus is accessible to theexogenously added antibody to recognize LC3. In one embodiment, theassay method takes advantage of this discovery and can conduct assays ofLC3 in blood samples of cells quickly, accurately and withoutpermeabilization of the cell (which can lead to inaccuracies). In thismethod, LC3 in a blood sample, including a plasma sample, is quantifiedand compared to a control or standard. The results can be used toevidence the existence or absence of an autophagy mediated disease stateor condition, provide an indication of the prognosis of treating adisease state (for example, by comparing the results to a control whichis obtained from a population of patients or subjects who have hadfavorable or unfavorable therapeutic results) or monitor therapy of anautophagy-mediated disease state with an autophagy modulator(autostatin) over a period of therapeutic intervention. This discoverymakes analysis readily amenable to immunohistochemistry, immunostaining,immunofluorescence and western blot assay. Also, the method can usemonoclonal or polyclonal antibodies, including especially in a sandwichassay in point of care facilities and/or home use.

Pursuant to this embodiment, blood from patients or subjects can bedrawn, and white blood cells (or more specifically different mononuclearcell populations, e.g. primary lymphocytes including CD4 and CDS cellsand their subsets) untreated or exposed. to starvation in a buffer(simple PBS or EBSS) for a period of time (between 10 minutes andseveral hours, often about an hour to an hour and a halt) and LC3 isdetected on the surface preferably by antibody staining (the antibodypreferably being conjugated to a reporter moiety which provides afluorescent or other signal which can be readily observed andoptionally, quantitated) without specifically permeabilizing the cells.Alternatively, in the assay method described above, the amount of LC3can be determined by a variety of techniques, includingimmunohistochemistry, immunostaining, immunofluorescence and westernblot assay. Also, the method can use monoclonal or polyclonalantibodies. In certain embodiments, the assay is a sandwich assay, anELISA assay or other antibody based assay, including a fluorometricand/or colorimetric assay which can be used at point of care facilitiesor at home.

Thus, the discovery related to external cell surface expressed LC3 formsthe basis for one or more of the following: (i) clinical tests forpatients (blood drawing and staining for LC3 on lymphocytes or wholewhite blood cells), (b) biomarkers in clinical studies (same as above),including providing a prognosis for therapy with a particular autostatinfor a particular autophagy-mediated disease state or condition, (iii)drug screening and development of approaches for the induction and/orinhibition of autophagy, and (iv) a target for treatment with blockingantibodies should LC3 on the cell surface show biological functions.Additional information may be found in the present specification asdescribed in detail herein. This discovery makes analysis is readilyamenable to immunohistochemistry, immunostaining, immunofluorescence andwestern blot assay. Also, the method can use monoclonal or polyclonalantibodies.

In one embodiment, the invention provides a method for identifying theexistence of compounds which exhibit activity consistent with modulationof autophagy such that the compounds may be useful in treating diseasestates or conditions which are mediated through autophagy. In thisembodiment of the invention, the method comprises exposing cellsexpressing LC3 to one or more compounds, including a library ofcompounds, and determining whether a compound or compounds bind to LC3wherein a compound which binds to LC3 is a potential modulator of LC3.In an alternative embodiment, the assay comprises determining whetherthe compound is an inhibitor or agonist of LC3 and therefore autophagy,for example, by determining whether the compound induces or inhibits theformation of LC3 puncta (as evidenced by the signal provided by afluorescent reporter such as green fluorescent green protein/FOP or redfluorescent protein/FRP as described in greater detail in the examplesherein), wherein a compound which induces the formation of LC3 punta isevidence that a tested compound is a potential therapeutic compound as amodulator (in this case, an agonist) of autophagy and a compound whichinhibits the formation of LC3 punta is evidence that a tested compoundis a potential therapeutic compound as a modulator (in this case, anantagonist) of autophagy. Once identified and further tested, thecompounds may be used as therapeutic agents in the treatment of diseasestates and/or conditions which are mediated through an autophagymechanism as otherwise described herein. In the assay method describedabove, the amount of LC3 can be determined by a variety of techniques,including immunohistochemistry, immunostaining, immunofluorescence andwestern blot assay. Also, the method can use monoclonal or polyclonalantibodies.

The present invention also relates to compounds which have beenidentified as modulators of autophagy (autostatins) which can be usedfor the treatment of an autophagy mediated disease state or condition.Thus, the present invention is also directed to pharmaceuticalcompositions which comprise an effective amount of at least one compoundidentified as an autophagy modulator in the assay described above,optionally in combination with a pharmaceutically acceptable carrier,additive or excipient and further optionally, at least one additionalbioactive agent. Such disease states or conditions, include, forexample, cancer, including metastasis of cancer, lysosomal storagediseases (discussed in detail hereinbelow), neurodegeneration(including, for example, Alzheimer's disease, Parkinson's disease; otherataxias), immune response, chronic inflammatory diseases, includinginflammatory bowel disease, including Crohn's disease, rheumatoidarthritis, lupus, multiple sclerosis, chronic obstructive pulmonydisease/COPD, pulmonary fibrosis, cystic fibrosis, Sjogren's disease;diabetes (I and II) and metabolic syndrome, liver disease, renal disease(including glomerular disease), cardiovascular disease (especiallyincluding ischemia, stroke, pressure overload and complications duringreperfusion), muscle degeneration and atrophy, symptoms of aging(including amelioration or the delay in onset or severity or frequencyof aging-related symptoms and chronic conditions including muscleatrophy, frailty, metabolic disorders, low grade inflammation,atherosclerosis and associated conditions such as cardiac andneurological both central and peripheral manifestations includingstroke, age-associated dementia and sporadic form of Alzheimer'sdisease, pre-cancerous states, and psychiatric conditions includingdepression.), stroke and spinal cord injury, arteriosclerosis,infectious diseases (microbial infections, including bacterial, fungal,cellular, viral (including influenza, herpes virus, HIV, HBV and HCV,among others) and parasitic infections, including protozoa! andhelminthic, including secondary disease states or conditions associatedwith infectious diseases), including AIDS and tuberculosis, amongothers, including in periodontal disease, development, both overlymature and immature development (including erythrocyte differentiation),embryogenesis/fertility and ageing/progeria. The common principle ofthis embodiment of the invention is that compounds, includingautostatins which are modulators (i.e., inhibitors or activators) ofautophagy (depending upon the disease) may be used alone or incombination with other agents, including other agents in a cocktail forthe treatment of the disease state and/or condition which is mediatedthrough autophagy.

In still other aspects of the invention, in one embodiment, theinvention provides a method of determining whether a subject suffersfrom, or is at risk of developing tuberculosis as defined hereinafter,including M tuberculosis, the method comprising determining a caspase-1level in a sample obtained from the subject and comparing the determinedcaspase-1 level to a control caspase-1 level (from a sample of one ormore healthy patients without tuberculosis or a sample of wherein anincrease or decrease in caspase-1 level indicates an increasedlikelihood that the subject suffers from or is at risk of developingtuberculosis. For example, this method can comprise the steps of:

(a) contacting a biological test sample obtained from the subject withan antibody or an antigen binding fragment thereof having specificbinding affinity for caspase-1, under conditions such that a complex canform between caspase-1 and the antibody or the antigen binding fragmentthereof;(b) measuring the amount of said complex, thereby determining the amountof caspase-1 in said biological test sample; and(c) comparing the amount of caspase-1 in said biological test sample toa standard or control sample;wherein an increased amount of caspase-1 in said biological test samplerelative to the standard or control sample is indicative of tuberculosisin said test sample.

The amount of caspase-1 in a biological sample can be determined by avariety of techniques, including immunohistochemistry, immunostaining,immunofluorescence and western blot assay. Antibodies used in themethods of the invention can be monoclonal or polyclonal antibodies.

In another embodiment, the invention provides a method of determiningwhether a subject suffers from, or is at risk of developing aninflammation-associated metabolic disorder as defined hereinafter, themethod comprising determining the level of one or more autophagy-relatedimmunomodulatory cytokines, alarmins or their regulators in a sampleobtained from the subject and comparing determined autophagy-relatedimmunomodulatory cytokine levels to control autophagy-relatedimmunomodulatory cytokine levels, wherein a decrease inautophagy-related immunomodulatory cytokine levels indicates anincreased likelihood that the subject suffers from or is at risk ofdeveloping an inflammation-associated metabolic disorder. For example,this method can comprise the steps of:

(a) contacting a biological test sample obtained from the subject withan antibody or an antigen binding fragment thereof having specificbinding affinity for an autophagy-related immunomodulatory cytokine asdefined hereinafter, under conditions such that a complex can formbetween the autophagy-related immunomodulatory cytokine and the antibodyor the antigen binding fragment thereof;(b) measuring the amount of said complex, thereby determining the amountof autophagy-related immunomodulatory cytokine in said biological testsample; and(c) comparing the amount of autophagy-related immunomodulatory cytokinein said biological test sample to a standard or control sample;wherein a decreased amount of autophagy-related immunomodulatorycytokine in said biological test sample relative to the standard orcontrol sample is indicative of an inflammation-associated metabolicdisorder in said test sample. This assay may be used alone or incombination with other assays in order to identify a particular diseasestate or condition to be treated.

In the assay method described above, the amount of autophagy-relatedimmunomodulatory cytokine can be determined by a variety of techniques,including immunohistochemistry, immunostaining, immunofluorescence andwestern blot assay. Also, the method can use monoclonal or polyclonalantibodies.

In a preferred embodiment of the method described above:

(1) the inflammation-associated metabolic disorder is selected from thegroup consisting of a hyperglycemic disorder (e.g. Type I and Type IIdiabetes, severe insulin resistance, hyperinsulinemia, insulin-resistantdiabetes (e.g. Mendenhall's Syndrome, Werner Syndrome, leprechaunism,and lipoatrophic diabetes) and dyslipidemia (e.g. hyperlipidemia asexpressed by obese subjects, elevated low-density lipoprotein (LDL),depressed high-density lipoprotein (HDL), and elevated triglycerides);(2) the autophagy-related immunomodulatory cytokine is selected from thegroup consisting of IL-1a, IL-1 B, IL-18, IL-12 p40 subunit, IL-4, M13,LMP1, EBNA2, IFN-y, ATG16L1, IRGMI, LC3B-II, HMGB1, TBK-1, GRASP-55 andGRASP-65, exocyst components regulating secretion of the said cytokinesand alarmins and mixtures thereof and (3) the method is conducted in ahigh-throughput, high-content imaging format as described hereinafter.

In still another embodiment, the invention provides a method ofscreening for a composition useful in the treatment of tuberculosis(e.g. M tuberculosis), the method comprising contacting a sample of atuberculosis-infected lung cell population with a candidate compositionand determining the extent to which the candidate compositiondown-regulates translation of caspase-1, wherein the candidatecomposition is identified as being potentially useful in the treatmentof tuberculosis if translation levels of caspase-1 in the sample areless than the comparable control values for an untreatedtuberculosis-infected lung cell population. For example, this method cancomprise the steps of:

(a) contacting a first sample of a tuberculosis-infected lung cellpopulation with a candidate composition;(b) determining one or more values representing the extent to which thecandidate composition down-regulates translation of caspase-1 in thefirst sample; and(c) comparing the determined one or more values to control values basedon translation levels of caspase-1 in a second, untreated sample of thecell population, wherein the candidate composition is identified asbeing potentially useful in the treatment of tuberculosis if translationlevels of caspase-1 in the first sample are less than the comparablecontrol values in the second sample.

In still another embodiment, the invention provides method of screeningfor a composition useful in the treatment of an inflammation-associatedmetabolic disorder, the method comprising contacting a sample of a cellpopulation evidencing a inflammation-associated metabolic disordermorphology with a candidate composition and determining the extent towhich the candidate composition up-regulates translation of one or moreautophagy-related immunomodulatory cytokines, wherein the candidatecomposition is identified as being potentially useful in the treatmentof an inflammation-associated metabolic disorder if translation levelsof the one or more autophagy-related immunomodulatory cytokines in thesample are less than the comparable control values for an untreatedsample of the cell population. For example, this method can comprise thesteps of:

(a) contacting a first sample of a cell population evidencing aninflammation-associated metabolic disorder morphology with a candidatecomposition;(b) determining one or more values representing the extent to which thecandidate composition down-regulates translation of one or moreautophagy-related immunomodulatory cytokines in the first sample; and(c) comparing the determined one or more values to control values basedon translation levels of one or more autophagy-related immunomodulatorycytokines in a second, untreated sample of the cell population, whereinthe candidate composition is identified as being potentially useful inthe treatment of an inflammation-associated metabolic disorder iftranslation levels of one or more autophagy-related immunomodulatorycytokines in the first sample are greater than the comparable controlvalues in the second sample.

In still another embodiment, the invention provides method ofdetermining whether a subject suffers from, or is at risk of developingan inflammation-associated metabolic disorder, the method comprising:

(a) contacting a biological test sample obtained from the subject withan antibody or an antigen binding fragment thereof having specificbinding affinity for LC3B-I or LC3B-II, under conditions such that acomplex can form between the autophagy-related immunomodulatory cytokineand the antibody or the antigen binding fragment thereof;(b) measuring the amount of said complex, thereby determining the amountof LC3B-I or LC3B-II in said biological test sample; and(c) comparing the amount of LC3B-I or LC3B-II in said biological testsample to a standard or control sample;wherein a difference in the amount of LC3B-I or LC3B-II in saidbiological test sample relative to the standard or control sample isindicative of an inflammation-associated metabolic disorder in said testsample. In this method, the biological test sample preferably is asample of white blood cells and the antibody is a purified monoclonalantibody (e.g. LC3B (DI 1) XP® Rabbit mAb #3868 from Cell SignallingTechnology, Inc., Danvers, Massachussets, USA),and wherein the antibody fragment is a fragment of such antibody. Also,the antibody or fragment thereof may also be used.

In still another embodiment, the invention provides a method ofdetermining whether a subject suffers from, or is at risk of developingtuberculosis (e.g. M tuberculosis), the method comprising determiningTBK-1 levels in a sample obtained from the subject and comparingdetermined TBK-1 levels to control TBK-1 levels, wherein a decrease inTBK-1 levels indicates an increased likelihood that the subject suffersfrom or is at risk of developing tuberculosis (e.g. M tuberculosis). Forexample, this method can comprise the steps of:

(a) contacting a biological test sample obtained from the subject withan antibody or an antigen binding fragment thereof having specificbinding affinity for TBK-1, under conditions such that a complex canform between TBK-1 and the antibody or the antigen binding fragmentthereof;(b) measuring the amount of said complex, thereby determining the amountof TBK-1 in said biological test sample; and(c) comparing the amount of TBK-1 in said biological test sample to astandard or control sample;wherein a decreased amount of TBK-1 in said biological test samplerelative to the standard or control sample is indicative of tuberculosisin said test sample.

In the method described above, the amount of TBK-1 can be determined bya variety of techniques, including immunohistochemistry, immunostaining,immunofluorescence and western blot assay and the antibody can be amonoclonal or polyclonal antibody.

In still another embodiment, the invention provides method of screeningfor a composition useful in the treatment of tuberculosis (e.g. Mtuberculosis), the method comprising contacting a sample of atuberculosis-infected lung cell population with a candidate compositionand determining the extent to which the candidate compositionup-regulates translation of TBK-1, wherein the candidate composition isidentified as being potentially useful in the treatment of tuberculosisif translation levels of TBK-1 in the sample are greater than thecomparable control values for an untreated tuberculosis-infected lungcell population. For example, this method can comprise the steps of:

(a) contacting a first sample of a tuberculosis-infected lung cellpopulation with a candidate composition;(b) determining one or more values representing the extent to which thecandidate composition up-regulates translation of TBK-1 in the firstsample; and(c) comparing the determined one or more values to control values basedon translation levels of TBK-1 in a second, untreated sample of the cellpopulation, wherein the candidate composition is identified as beingpotentially useful in the treatment of tuberculosis if translationlevels of TBK-1 in the first sample are greater than the comparablecontrol values in the second sample.

In still another embodiment, the invention provides a method ofscreening a composition for an autophagy-associated effect oncytoplasmic puncta of either (1) tuberculosis-infected lung cells, or(2) cells implicated in a lipid-related metabolic disorder, the methodcomprising:

(a) culturing a sample of the cells;(b) plating the cell sample on multi-well plates;(c) contacting the cell sample with the composition; and(d) using high-content imaging to examine the cell sample for anautophagy-associated effect on cytoplasmic puncta, wherein the method isconducted using a high-throughput format.

In a preferred embodiment of the high-content imaging method describedabove (any embodiment, especially including those embodiments related toidentifying autostatins as otherwise described herein), the multi-wellplates are 384-well plates, the cells are transfected with RFP-LC3 orGFP-LC3 prior to plating, the cytoplasmic puncta are RFP-LC3 puncta orGf P-LC3 puncta, and the composition is selected from a chemical librarysuch as Prestwick chemical library or the Torrey Pines Institutelibrary. In another preferred embodiment, this method includes comparingthe autophagy-associated effect on cytoplasmic puncta in cell samplesthat have been contacted with the composition and the morphology ofpositive control cell samples that have been contacted with eitherpp242, rapamycin or other mTor inhibitor as described herein, or thathave been starved.

In still another embodiment, the invention provides a method of treatinga subject who has been infected with tuberculosis (e.g. M tuberculosis)or who is at risk of such infection, the method comprising administeringto the subject a pharmaceutically effective amount of a caspase-1inhibitor as defined hereinafter.

In still another embodiment, the invention provides a method of treatinga subject who suffers from an inflammation-associated metabolic disorderor who is at risk of developing such a disorder, the method comprisingadministering to the subject a pharmaceutically effective amount of aTBK-1 agonist as defined hereinafter.

In still another embodiment, the invention provides a method of treatinga subject who has been infected with tuberculosis (e.g. M tuberculosis)or who is at risk of such infection, the method comprising administeringto the subject a pharmaceutically effective amount of a TBK-1 agonist(e.g. a vascular disrupting agent (VDA) such as lavone acetic acid andits derivatives, e.g., 5, 6-dimethylxanthenone-4-acetic acid (DMXAA)).

In still another embodiment, the invention provides a kit comprising:

(a) at least one reagent which is selected from the group consisting of(i) reagents that detect a transcription product of the gene coding fora TBK-1 protein marker or autophagy-related immunomodulatory cytokine asdescribed herein (ii) reagents that detect a translation product of thegene coding for TBK-1 or an autophagy-related immunomodulatory cytokine,and/or reagents that detect a fragment or derivative or variant of saidtranscription or translation product;(b) instructions for diagnosing, or prognosticating either an infectionby tuberculosis (e.g. M tuberculosis) or the presence of aninflammation-associated metabolic disorder, or determining thepropensity or predisposition of a subject to develop either tuberculosis(e.g. M tuberculosis) or an inflammation-associated metabolic disorderor of monitoring the effect of a treatment of a tuberculosis (e.g. Mtuberculosis)-related infection or an inflammation-associated metabolicdisorder.

In still another embodiment, the invention provides a kit comprising:

(a) at least one reagent which is selected from the group consisting of(i) reagents that detect a transcription product of the gene coding forcaspase-1 marker or an autophagy-related immunomodulatory cytokine asdescribed herein (ii) reagents that detect a translation product of thegene coding for caspase-I or an autophagy-related immunomodulatorycytokine, and/or reagents that detect a fragment or derivative orvariant of said transcription or translation product;(b) instructions for diagnosing, or prognosticating either anautophagy-related immunomodulatory cytokine or infection by tuberculosis(e.g. M tuberculosis), or determining the propensity or predispositionof a subject to develop an autophagy-related immunomodulatory cytokineor to contract a tuberculosis (e.g. M tuberculosis)-associated infectionor of monitoring the effect of a treatment of a tuberculosis (e.g.tuberculosis)-associated infection.

In still another embodiment, the invention provides a pharmaceuticalcomposition comprising:

(a) an autophagy-related immunomodulatory cytokine antagonist; andoptionally(b) a pharmaceutically-acceptable excipient.

In still another embodiment, the invention provides a pharmaceuticalcomposition comprising:

(a) an autophagy-related immunomodulatory cytokine agonist; andoptionally(b) apharmaceutically-acceptable excipient.

In still another embodiment, the invention provides a pharmaceuticalcomposition comprising:

(a) a caspase-1 or TBK-1 antagonist; and optionally(b) apharmaceutically-acceptable excipient.

The autophagy-related methods disclosed herein therefore provideversatile approaches to the diagnosis and treatment of a wide variety ofdiseases that to date have remained difficult to identify and treat.These and other aspects of the invention are explained further in theDetailed Description of the Invention.

BRIEF DESCRIPTION OF THE FIGURES Figures for Example 1

FIG. 1. Autophagy protects from excessive inflammation in a mouse modelof tuberculosis infection. (A) Weight loss in Atg^(5fl/fl) LysM-Cre+ andAtg^(5fl/fl) LysM-Cre− mice infected with M tuberculosis H37Rv (e³ dose;see Suppl. Table 1). (B) Gross lung pathology (e³ dose). (C) Lunghistological sections (e³ dose, day 36). Panels: i-iv, H&E stain(arrows, necrotic lesions); v and vi, acid-fast staining (arrows,bacilli; insets enlarged area). (D) Survival of Atg^(5fl/fl) LysM-Cre+and Atg^(5fl/fl) LysM-Cre− mice infected with M tuberculosis H37Rv (e4dose). (E) Weight loss in Atg^(5fl/fl) LysMCre+ and Atg^(5fl/fl)LysM-Cre− mice infected with M tuberculosis H37Rv (e4 dose). Data,means±SE, **p<0.01 (t test). Mouse survival statistics: Kaplan-Meiersurvival analysis with the Log-Rank method.

FIG. 2. Intrinsically activated phenotype of lung macrophages andneutrophilic infiltration in uninfected Atg5fl/fl LysM-Cre+ mice. (A, B)Flow cytometric quantification of macrophages per organ tissues inuninfected Atg^(5fl/fl) LysM-Cre+ and Atg^(5fl/fl) LysM-Cre− mice. (C)Activation state of macrophages measured by surface markers CD1 d, MHCII, DEC205 and CD86 in the lungs of uninfected Atg^(5fl/fl) LysM-Cre−(left plots) and Atg^(5fl/fl) LysM-Cre+ mice (right plots). (D, E) PMNquantification in the lungs and bone marrow of uninfected Atg5fl/flLysM-Cre+ and Atg^(5fl/fl) LysM-Cre− mice. Data, means±SE, n≧3, *p<0.05,¶>0.05 (t test).

FIG. 3. Excess cytokine secretion is a cell-autonomous property ofautophagy-deficient macrophages. (A-C) Multiplex cytokine detection byLuminex in the lungs of M tuberculosis H37Rv infected Atg^(5fl/fl)LysM-Cre+ and Cre− mice (e2 dose, 102 CFU); shown: IL-1α, CXCLI, andIL-12p70 (see Suppl. Fig. S3 for additional cytokines). (D-F) In vitrocytokine (IL-1 u, CXCL1, and IL-12p70) release (ELISA) fromLPS+IFN-γ-stimulated Atg^(5fl/fl) LysM-Cre+ and Cre− bone marrow-derivedmacrophages (BMM). (G,H) IL-1α and CXCL1 levels (ELISA) in lunghomogenates of uninfected Atg5fl/fl LysM-Cre+ and Cre− mice. Data,means±SE, n≧3, *p<0.05,**p<0.01 (t test).

FIG. 4. Autophagy regulates IL-1a release. (A,B) IL-1α (ELISA) releasedfrom LPS+IFN-γ stimulated Atg5^(fl/fl) LysM-Cre+ and Atg5^(fl/fl)LysM-Cre− BMM in the presence of 50 μg/ml rapamycin (Rap), 10 mM 3-MA,or 100 nM Bafilomycin A1 (Baf A1) after 12 h of stimulation. (C) IL-1α(ELISA) in culture supernatants of cells as in A, treated with calpaininhibitor, ALLN (100 μM). (D-F) Images and quantification of cellspositive for LC3-only, IL-1α-only or LC3+IL-1α. Cells, wild type (Atg5+)BMM stimulated with LPS+IFN-γ and incubated for 90 min in EBSS in theabsence (D, control) or presence (E, Baf A1) of bafilomycin A1. Cutofffor cells to be considered positive: >6 red or green puncta. Redarrowheads, IL-1α+LC3− cells; green arrowheads, IL-1α− LC3+ cells; 10μm. Data, means±SE; n≧3; *p<0.05, **p<0.01, †>0.05 (t test).

FIG. 5. Active caspase-1 is a target for autophagy. (A) Confocalmicrocopy analysis of caspase-1 colocalization relative to LC3 inGFP-LC3 expressing BMM induced for autophagy by starvation (EBSS) in thepresence of bafilomycin A1 for 90 minutes. Scale bar, 5 μM; Arrowheadsand insets, LC3+ caspase-1+ positive profiles (colocalization). (B)Pearson's colocalization coefficient for caspase-1 vs. LC3 and IL-1α vs.LC3. (C) Caspase-1 accumulation in Atg5^(fl/fl) LysM-Cre− orAtg5^(fl/fl) LysM-Cre+ BMM induced for autophagy in EBSS with or withoutbafilomycin A1 (BafA1) and subjected to Western blot analysis. (D) IL-1α(culture supernatant ELISA) released from Atg5fl/fl LysM-Cre+ andAtg5fl/fl LysM-Cre− BMM incubated overnight with 100 ng/ml LPS andexposed for 1 h to inflammasome agonist silica (250 μg/ml) in EBSS.Data, means±SE, n≧3; **p<0.01 (t test).

FIG. 6. IL-17 phenotype in CD4 T cells from Atg5fl/fl LysM-Cre+ mice.(A) CD44 and CD25 expression on CD4 T cells from lungs of uninfectedAtg5^(fl/fl) LysM-Cre+ and Atg5^(fl/fl) LysM-Cre− mice. (B,C)Intracellular levels of IL-17A (top panel) and IFN-γ (bottom panel) inCD4 T cells isolated from lungs of uninfected Atg5^(fl/fl) LysM-Cre+ andCrc-mice and stimulated with phorbol 12-myristate 13-acetate andionomycin ex vivo in the presence of brefeldin A and monensin. (D) DTHreaction (footpad induration) in BCG-infected Atg5^(fl/fl) LysM-Cre+ andAtg5^(fl/fl) LysM-Cre− mice footpad-injected with the synthetic PPD atday 21 postinfection. Data, percent change (footpad thickness) uponchallenge with the synthetic PPD relative to the contralateralPBS-challenged footpad. (E,F) Cytokine production (IL-17A and IFN-γ;ELISA) by splenocytes from Atg5^(fl/fl) LysM-Cre+ and Atg5^(fl/fl)LysM-Cre− mice (day 23 post-infection with BCG) re-stimulated for 3 daysex vivo with the synthetic PPD. (G) Intracellular IL-17A production (day4; release blocked with monensin) by naïve CD4 T cells polarized in thepresence of cytokine cocktails: 5 ng/ml TGF-β and 20 ng/ml IL-6, plus 20ng/ml IL-1α or 20 ng/ml IL-1β. Dot plot, levels of IL-17A inunstimulated cells (starting material). Histograms, IL-17A in naïve CD4T cells polarized in the presence of TGF-β, IL-6 and IL-1α or TGF-β,IL-6 and IL-1β. (H) Percent of IL-17A+CD4 T cells under respectivepolarizing conditions. Data: means±SE; n≧3; **p<0.01; †, p>0.05 (ttest).

FIG. 1T. Tabular summary of results of mouse tuberculosis experiment ofExample 1.

FIGS. 1-6 (Supplementary). Pathology, immunoblotting, detection assayand flow cytometry results of mouse tuberculosis experiment of Example1.

Figures for Example 2

FIG. 1X2. Analysis of the complete set of murine Rab and Rab-likefactors for effects on cell-autonomous autophagic elimination ofmycobacteria and the role of Rab8b. A. Sixty-two Rab or Rab-like factorsencoded by the Mus musculus genome were knocked down by siRNA inRAW264.7 macrophages (details and identity of each bar in Supple. Table1S), macrophages infected with M. tuberculosis var. bovis BCG, autophagyinduced by starvation (Starv), and autophagic killing of BCG quantified.Increase in BCG survival indicates decrease in autophagic killing. Ser,scrambled (control) siRNA. B-D. Effect of Rab8b knockdown on maturationof BCG phagosomes into autophagolysosomes. LTR, Lysotracker Red(acidotropic dye); CathD, cathepsin D. E-F. Validation of the role forRab8b in autophagic killing of BCG. BCG survival, % of BCG CFU recoveredfrom RAW 264.7 macrophages pretreated with siRNAs; si Scr, conrolscrabled siRNA; si Rab8b, Rab8bsiRNA; Full, full medium; Starve,autophagy induced by starvation. Data, means±se (n≧3; †, p≧0.05*,p<0.05; **, p<0.01; ANOVA).

FIG. 2X2. Role of TBK-1, a Rab8b downstream effector, in autophagicmaturation. A. Rab8b effector cascade. Double headed arrows, proteininteractions. Arrows, processes downstream of TBK-1 (autophagyconnection established here). Htt, Huntingtin (normal, without expandedGlu repeats). B. Role of downstream effectors of Rab8b in autophagickilling of BCG. BCG survival, % of BCG CFU recovered from RAW 264.7macrophages pretreated with siRNAs. Full, full medium (controlconditions); si Scr, scrambled siRNA (control siRNA); Starve, autophagyinduced by starvation; si TBKI, siRNA to TBK1. C. Effect of TBK-1inhibitor BX795 on acidification of BCG-containing organelles followinginduction of autophagy. RAW 264.7 macrophages were pretreated with 10 nMBX795, infected, and induced for autophagy by starvation (Starve). D.Autophagic killing of BCG in RAW 264.7 macrophages pretreated withBX795. BCG survival, % CFU recovered from RAW 264.7 cells. E,F. RAW264.7 expressing RFP-GFP-LC-3 and pretreated with scrambled or TBK-1siRNAs were untreated (Full) or induced (Starv) for autophagy. Puncta;R+G+(RFP+ GFP+), early autophagic organelles; R+G−(RFP+ GFP−), lateautophagic organelles. Images, merged red and green channels. G,H.Effects of TBK-1 on LC3-II levels and degradation during autophagicmaturation. Tbk-1−/− and Tbk-1+/+ MEFs were uninduced and induced forautophagy, treated or not treated with bafilomycin A1 (BafA1) to inhibitautophagic degradation of LC3-II. Data, means±se (n≧3; †, p≧0.05*,p<0.05; **, p<0.01; ANOVA).

FIG. 3X2. IL-1β-induced autophagy eliminates intracellular mycobacteriain a process dependent on TBK-1. A. RAW264.7 macrophages weretransiently transfected with EGFP-LC3 and treated with 10 ng/ml murineIL-1β for 2 h, and 27 assayed for LC3 puncta formation by confocalmicroscopy (only puncta ≧1 μm were scored as positive). B. RAW264.7macrophages transfected with mRFPGFP-LC3 tandem probe, treated with 10ng/ml IL-1β for 2 h were scored for number (per transfected cell) ofRFP+ GFP+ puncta (R+G+; early autophagosomes), RFP+ GFP−(R+G−;autolysosomes), and total LC3 puncta. C. Immunoblot analysis ofendogenous LC3 conversion to lipidated form (LC3-II) in RAW 264.7 murinemacrophages upon treatment with 10 ng/ml IL-1β for 2 h, in the absenceor presence of bafilomycin A1. Graph, ratio of LC3-II to actin intensityin immunoblots from bafilomycin A1-treated samples. D. RAW264.7 murinemacrophages were co-transfected with tandem mRFP-GFP-LC3 probe andexpression constructs containing either wild-type MyD88 (MyD88-WT) or adominant-negative mutant of MyD88 (MyD88-DN). Following stimulation with10 ng/ml IL-1β for 2 h, LC3 puncta were quantified as in B. E. Inductionof autophagy in response to IL-1β is abrogated in bone marrow-derivedmacrophages (BMM) from MyD88 knockout (MyD88−/−) mice, measured byratios of LC3-II band relative to actin following treatments of BMMs andimmunoblotting of cellular extracts. F. Proteolysis of stable proteins(radiolabeled by a pulsechase protocol) upon stimulation of RAW264.7cells with 10 ng/ml IL-1β for 2 h (Full+IL-1β) relative to control(Full) or starvation-induced autophagy (Starve). G. Mycobacterialkilling as a measure of autophagic endpoint is induced by IL-Iβ.RAW264.7 macrophages were knocked down for Atg7 (by Atg7 siRNAtransfection 48 h prior to infection), infected with M. tuberculosisH37Rv for 1 h, washed and then left untreated or treated with 10 ng/mlrecombinant murine IL-1b for 2 h after which they were lysed and platedfor colony forming units determination, and survival expressed relativeto sample transfected with control scrambled siRNA and not treated withIL-1β. Immunoblots, Atg7 knockdown and levels of Atg5-Atg12 complexes.Data, means±se, except in E where data are means±sd (n≧3; †, p0.05*,p<0.05; **, p<0.01; ANOVA).

FIG. 4X2. Requirement for TBK1 in IL-1β mediated autophagic killing ofBCG. A. BCG survival, % CFU recovered from RAW264.7 macrophagespretreated with IL-1β with and without 10 nM BX795 treatment. B. BCGsurvival in infected RAW264.7 (and knocked down or not for TBK-1)macrophages stimulated with IL-1β. C-F. Requirement for TBK-1 in IL-1βinduced autophagy. RAW264.7 macrophages were incubated in full medium(Control) or induced by adding IL-1β to full medium. Cells werepretreated with 10 nM BX795 where indicated. Macrophages were treatedwith or without bafllomycin A1 (BafA1) to inhibit autophagic degradationof LC3-II, and cellular extracts analyzed by imunoblotting. Graphs,densitometric analyses of LC3-II levels normalized to actin levels(LC3-II/Actin) were plotted. Data, means±se (n=3; †, 0.05; **, p<0.01;ANOVA).

FIG. 5X2. Rab8b and its downstream effector TBK-1 co-immunoprecipitateand colocalize with autophagic organelles. A. HEK 293T cell extracts,transiently transfected with control (EGFP), GFP-Rab8b (Wt, wild type)and GFP-Rab8b Q67L (Q67L, constitutively active) expression constructswere immunoprecipitated with anti-GFP antibody; immunoblots for immunecomplexes and inputs were probed with anti-TBK-1 and anti-GFPantibodies. B. Colocalization of Rab8b and its downstream effector,TBK-1 with the basal autophagic machinery factor LC3. Florescence;endogenous TBK-1 (red, Alexa568), Rab8B (green, Alexa488), LC3 (blue,Alexa633). Cells (mouse primary bone marrow macrophages; BMM) wereinduced for autophagy by starvation in the presence of bafilomycin A1 toinhibit autophagic maturation and degradation. Arrows, colocalization ofRab8b, TBK-1, and LC3. C. Representative line tracing of threefluorescence channels in images in A. D. TBK-1 colocalization with theautophagic adaptor sequestosome 1/p62 and LC3. Cells (BMM), treatments,labels and graphs as in a and b. Arrows, colocalization of TBK-1, p62and LC3. Cells (BMM) were induced for autophagy by starvation in thepresence of bafilomycin A1 to inhibit autophagic maturation. E.Representative line tracing of fluorescence channels in images in C.Data, representative of ≧3 independent experiments.

FIG. 6X2. TBK-1 co-fractionates and colocalizes on intracellularmembranous organelles with autophagic adaptors and machinery. Analysisby subcellular fractionation of the assembly of Rab8b-TBK-1 andautophagic machinery in resting cells or upon induction of autophagy (bystarvation). RAW 264.7 macrophages uninduced (A) or induced (B) forautophagy were subjected to subcellular fractionation of organelles byisopycnic sucrose density gradient centrifugation. PNS, postnuclearsupernatant. 1-4, pooled fractions. Rectangle over fraction 9,convergence in autophagic organelles (LC3-II) of: Rab8b, TBK-1, UVRAG(Beclin 1 interacting protein specific for autophagosomal maturation),and autophagic adapters p62 and NDP52. Refractive indexes below thelanes reflect sucrose density of each fraction. C. Images; endogenousUVRAG (Alexa568), endogenous TBK-1 (Alexa488). Cells, BMM, uninduced(Full) and induced (Starvation) for autophagy. D. Pearson's coefficientof TBK-1 and UVRAG colocalization. E. TBK-1 colocalization withautophagic adaptors in BMM. Images: endogenous TBK-1 (Alexa568; red),p62 (Alexa488; green), NDP52 (Alexa633; blue) and merged. Line tracing,analysis of colocalization of TBK-1 (red tracing), p62 (green tracing)and NDP52 (blue tracing). F,G. Pearson's colocalization coefficients forTBK-1-p62 and TBK-1-NDP52. Data, means±se (n=3, three independentexperiments with at least 5 images analyzed per experiment; †, p≧0.05;**, p<0.01; ANOVA).

FIG. 7X2. TBK-1 controls p62 phosphorylation, and affects autophagicclearance of p62 and its cargo capture, delivery and degradation. A-C.High content imaging analysis (using Cellomics high-content microscopysystem) of p62 puncta (endogenous, revealed by imunofluorescence) in BMMwith or without treatment with TBK-1 inhibitor BX795. Panel A showsoutput from Cellomics high-content microscopy and analysis softwarecomparing the number 29 of p62 puncta between TBK-1 inhibitor-treated(BX795) and control (DMSO) BMM. Vertical axis denotes the mean number ofp62 puncta per cell and horizontal axis denotes the position of the well(B, BX795 series; C, control series) on the plate. Between 754 and 2395cells were analyzed per well. Panel C shows t test (data, means±se; **,p<0.01) from cumulative data treating only whole wells as independentsamples (n=4). D. Effects of TBK1 pharmacological inhibitor, BX795 onp62 levels. Tbk-1+/+ MEFs were treated with BX795; bafilomycin A1(BafA1) to inhibit autophagic degradation. Densitometric analyses of p62levels normalized against actin levels were plotted (n=2; error bars,range). E. TBK-1 is necessary for efficient autophagic clearance of polyubiquitinated proteins. Cell lysates from Tbk-1+/+ and Tbk-1−/− MEFsuninduced and induced for autophagy by starvation were incubated withTUBE2 agarose beads and bound material pulled down. Western blots wereprobed for K63 polyubiquitin chains. F-H. Identification ofTBK-1-dependent 5403 phosphorylation of the UBA domain of p62. In vivophosphorylation of p62 UBA domain following cotransfection ofGFP-p62D69A (D69A mutation prevents oligomerization with endogenous p62)and expression constructs of TBK-1 wild type or kinase defective form.Immunoprecipitated (GFP-p62) material was subjected to tandem massspectrometry. A triply charged ion with the mass 857.01 was selected forfragmentation. This ion was identified as the phosphorylatedLIESLSQMLpSMGFSDEGGWLTR peptide (shown in panel H) from p62. Panel Gshows MS spectra from LC-MS, showing the phosphopeptide of 857.01 tri/zobserved in p62 phosphorylated by TBK1. The peptide was not observedwhen GFP-p62 was co-transfected with the kinase-defective K38D mutant ofTBK1. Spectra are taken from the same retention time in both runs,confirmed by the unspecific peaks observed in both spectra. I. HEK293cells transfected with vector control, myc-TBK-1 or myc-TBK-1 K38D wereleft untreated or were treated for 2 h with 1 μm BX795. Cell extractswere immunoblotted with antibodies against phospho-p62 (S403), p62, mycand actin. Abbreviations: end. p62, endogenous p62. J. MBP or MBP-taggedp62 proteins were expressed and affinity-purified from E. coli. TBK-1mediated phosphorylation was assessed by incubating recombinant MBP,MBP-p62 or MBP-p62 S403A with recombinant active TBK-1 in the presenceof [γ-32P] ATP for 10 min at 30° C. The reaction products were analyzedby autoradiography (AR). CBB, Coomassie Brilliant Blue staining.

FIG. 8X2. Additional Rabs displayed a range of effects on autophagickilling of BCG, including those Rabs previously implicated in autophagy.

Suppl. FIG. 1S. Analysis of the effect of Rab34 on autophagy. A. Rab34knockdown elevates proportion of autolysosomes under basal conditions.RAW264.7 macrophages, knocked down for Rab34 by siRNA and expressingRFP-GFP-LC3, were quantified for early (G+R+) and acidified late (G-R+)autophagic organelles. Note an increase in G-R+LC3 puncta underuninduced (Full) conditions and no increase relative to scramble siRNAcontrol under induced (starvation) conditions. B. Rab34 increases BCGsurvival (relative to Full control) under both uninduced (Full) andinduced (Starve) conditions. C. A monolayer of cells (unpermeabilized)stained for CD98. D. Flow cytometry analysis of CD98 expression. E.Rab34 is required for CD98 (amino acid importer) expression on plasmamembrane. CD98 was stained in unpermeabilized (external) andpermeabilized (internal) cells and fluorescence examined by imaging andquantified by line tracing intensity. F. Uptake of [3H] Leu by cellsknocked down for Rab34. RAW264.7 macrophages were transfected withcontrol (Scr) and Rab34 siRNA (for 48 h) and DMEM supplemented with 1μCi/ml tritiated L-Leucine was added to cells. Samples for uptake weretaken at 0.5 and 2 h. At each time point, cells were washed quicklythree times in PBS, hypotonically lysed and measured for totalradioactivity using liquid scintillation. Uptake was normalized tocontrol siRNA treated cells. G. Membrane permeant form of pyruvate(methyl pyruvate) employed as previously described (Lum et al., 2005)for nutritional bypass restores LC3-II levels in cells knocked down forRab34. H. Role of Rab8a in autophagic killing of BCG. Knockdown of Rab8ashows a trend but no statistical significance in protecting BCG formautophagic killing. Rab8a knockdown analyzed by immunoblotting. Data,means and standard errors (n=3); *, p<0.05; †, p≧0.5 (ANOVA).

Suppl. FIG. 2S. TBK-1 is required for autophagic maturation. A. Effectsof TBK-1 absence or presence on LC3-II levels in mouse embryonicfibroblasts (MEFs). Tbk-1−/− and Tbk-1+/+ MEFs were uninduced andinduced for autophagy, treated or not treated with 100 nM bafilomycin A1(BafA1) to inhibit autophagic degradation of LC3-II under basalconditions (Full) or during 90 min of starvation in EBSS (Starve). B,C.Effects on LC3-II levels of BX795, a pharmacological inhibitor of TBK1.Tbk-1+/+ MEFs, untreated or treated with 10 nM BX795 (16 h) in thepresence or absence of 100 nM bafilomycin A1 (BafA1; 2 h) were subjectedto immunoblotting analysis. Ratio of LC3-II/actin band intensity. Data,means±se (n=3; †, *, p<0.05; **, p<0.01; t-test). D,E. Although attemptsto complement the absence of TBK-1 in Tbk1−/− MEFs by transfection withTbk-1 expression constructs was hampered by low transfection efficiency,overexpresion of Tbk-1 transgene in RAW 264.7 cells caused alterationsin LC3-II levels, which diminished faster with time in Tbk-1transgeneexpressing cells relative to untransfected cells.

Suppl. FIG. 3S. TBK1 is required for cathepsin D delivery toautophagolysosmes and conventional phagosomes and IL-1β inducesautophagy in primary murine and human macrophages. A,B. RAW 264.7macrophages pretreated with siRNAs, after ingestion of 1 μm magneticbeads were either induced (A) or uninduced (B) for autophagy bystarvation. MBP, previously characterized magneticbeadautophagolysosomal organelles 2 (Ponpuak et al., 2010). Delivery ofcathepsin D was determined by immunoblotting. PNS, post-nucelarsupernatant. C. Macrophages derived from bone marrows obtained fromfemurs of EGFP-LC3 knock-in mice were treated with 10 ng/ml recombinantmurine IL-1β and LC3 puncta quantified. D. Immunoblot analysis of LC3-IIformation, in human monocyte-derived macrophages treated with 10 ng/mlhuman recombinant IL-1β. Data, means±se (n=3; *, p<0.05; t-test).

Suppl. FIG. 4S. Rab8b and TBKI colocalize with autophagic machinery.A,B. Endogenous proteins in BMM as in FIG. 5 were imaged in cellsincubated in indicated conditions: Full, complete medium; Full+BafA1,complete medium supplemented with bafilomycin A1; Starv, autophagyinduced by starvation (EBSS); Starv+BafA1, autophagy induced bystarvation in the presence of bafilomycin A1. When treated with BafA1,the purpose was to inhibit autophagic maturation and degradation.Triangles in insets, colocalization of all three fluorescent probes.

Suppl. FIG. 5S. TBK-1 renders p62 competent for entry into the autophagypathway. Immunoblot of cell lysates from Tbk-1−/− and Tbk-1+/+ MEFs,uninduced (Full) and induced (Starve) for autophagy, untreated ortreated with bafilomycin A1 (BafA1). Immunoblot was developed using p62antibody.

Figures for Example 3

FIG. 1X3. Induction of autophagy enhances IL-1β secretion. (A) Atg5fl/flCre⁻ and Atg^(5fl/fl) Cre bone marrow-derived macrophages (BMMs),pretreated overnight with 100 ng/ml LPS, were stimulated for 1 h withthe inflammasome agonist nigericin (20 mM) with (Starvation; EBSS) orwithout (Full; full medium) autophagic induction. Cell culturesupernatants were assayed for murine IL-1β by ELISA. Data represent meanvalues±s.d. (nX3); *Po0.05. (B) LPS-pretreated Atg5fl/fl Cre− andAtg^(5fl/fl) Cre⁺ BMMs were stimulated with 20 mM nigericin for 1 h inOptiMEM and the release of active caspase-1 and IL-1β was determined byimmunoblotting. (C) As in (A), assayed for IL-18. Data represent meanvalues±s.d. (nX3); *Po0.05. (D) LPS-pretreated BMMs were exposed to alum(250 mg/ml) for 1 h with or without autophagic induction by starvation.Secreted IL-1β was measured as in (A). Data represent mean values±s.d.(nX3); *Po0.05. (E) LPS-pretreated BMMs were exposed to silica (250mg/ml) for 1 h with or without autophagic induction by starvation.Secreted IL-1β was measured as in (A). Data represent mean values±s.d.(nX3); *Po0.05. (F) BMMs were transfected with scramble (Scr) controlsiRNA or siRNAs against ASC andNLRP3. After 48 h following transfection,cells were treated overnight with LP S and subjected to nigericin (20mM) and starvation for 1 h. Data represent mean values±s.d. (nX3);*Po0.05. (G) Immunoblot analysis of ASC and NLRP3 knockdowns. (H) BMMswere transfected with scramble (Scr) control siRNA or siRNAs against ASCand NLRP3. After 48 h following transfection, cells were treatedovernight with LPS and subjected to silica (250 mg/ml) and starvationfor 1 h. Data represent mean values±s.d. (nX3); *P00.05. (I)Colocalization of IL-1β with the basal autophagic machinery factor LC3.Fluorescence: LC3 (green, Alexa488); IL-1β (red, Alexa568). BMMs werefrom GFP-LC3 knock-in mice, treated with LPS then prepared forimmunofluorescence microscopy using fluorescently labelled antibodiesagainst GFP and IL-1b. (J, K) A line fluorescence tracing from images in(I). (L) Pearson's colocalization coefficient for IL-1β and LC3.Pearson's coefficient was derived from three independent experimentswith five fields per experiment, for a total of 15 fields contributingto the cumulative result.

FIG. 2X3 Autophagic pathway progression promotes secretion ofinflammasome substrates. (A, B) LPS-pretreated BMMs were treated with 20mM nigericin (Nig) and 100 nM bafilomycin A1 (Bat) with (Starvation) orwithout (Full) autophagic induction for 1 h and secreted IL-1β (A) andIL-18 (B) were measured. Data represent mean values±s.d. (nX3); *Po0.05.(C) LPS-pretreated BMMs were treated with 250 mg/ml of silica and 100 nMbafilomycin A1 (Bat) with (Starvation) or without (Full) autophagicinduction for 1 h and secreted IL-1β were measured. Data represent meanvalues±s.d. (nX3); *Po0.05. (D) Colocalization of cathepsin B with thebasal autophagic machinery factor LC3 and IL-1b. Fluorescence; LC3(green, Alexa4S8), IL-1β is (red, Alexa568), and cathepsin B (blue,Alexa633). BMMs from GFP-LC3 knockin mice were treated with LPS and thenanalysed for immunofluorescence. (E) Colocalization line tracinganalysis from images in (D). (F) LPS-pretreated BMMs were treated with20 mM nigericin and cathepsin B inhibitor CA-074 Me (10 rnM), with(Starvation) or without (Full) autophagic induction, for 1 h andsecreted IL-1β was measured. Data represent mean values±s.d. (nX3);*Po0.05. (G) LPS-pretreated Atg^(5fl/fl) Cre⁺ and Atg^(5fl/fl) Cre⁻ BMMswere stimulated with 20 mM nigericin for 1 h in OptiMEM and release ofcathepsin B was determined by immunoblotting.

FIG. 3X3. Rab8a is required for autophagy-activated IL-111 secretion.(A) Colocalization of Rab8a with the basal autophagic machinery factorLC3 and IL-1b. Fluorescence; LC3 (green, Alexa488), IL-1β (red,Alexa568), Rab8a (blue, Alexa633). BMMs from GFP-LC3 knock-in mice werepretreated with LPS and analysed by immunofluorescence microscopy.Arrows indicate triple colocalization. (B) Line tracing analysis offluorescence signal intensity. (C) Pearson's colocalization coefficientfor IL-1β and Rab8a. Pearson's coefficients were derived from threecompletely independent experiments with 45 fields per experiment, for atotal of ×15 fields contributing to the cumulative result. (D) BMMs weretransfected with siRNAs against Rab8a or scramble (Scr) control. At 24 hafter the first transfection, cells were transfected again with siRNA,treated with LPS and the day after subjected to nigericin in full mediumfor 1 h, and IL-1β secretion measured. (E) Immunoblot analysis of Rab8aknockdown in BMMs. (F) RAW264.7 macrophages were transfected withGFP-tagged Rab8a constructs (WT, wild type; S22N, dominant-negativemutant), treated overnight with LPS and stimulated for 1 h with 20 mMnigericin along with induction of autophagy by starvation. IL-1βsecretion was measured by ELISA. Data represent mean values±s.d. (nX3);*Po0.05.

FIG. 4X3. GRASP55 is required for autophagy-activated IL-1β secretion.(A) BMM cells were transfected with scramble (Scr) control siRNA orsiRNA against GRASP55. After 48 h of transfection, cells were treatedwith LPS and the day after subjected to 20 mM nigericin in EBSS, andsecreted IL-1β was measured by ELISA. Data represent mean values±s.d.(nX3); *Po0.05. Inset: Immunoblot analysis of GRASP55 knockdown. (B)Immunofluorescence confocal microscopy analysis of LC3 and GRASP55distribution. LCT (green, Alexa488), GRASP55 (red, Alexa568). BMMs werepretreated overnight with 100 ng/ml LPS and either not stimulated (Ctrl)or stimulated (Nig) for 30 min with the inflammasome agonist nigericin(20 mM) in full medium. (C) Line tracings, analysis of fluorescencesignal intensity from images in (B). (D) Pearson's coefficients for LC3and GRASP55 were quantified using SlideBook morphometric analysissoftware as a measure of adjacency between GRASP55 and LC3 profiles.Pearson's coefficients were derived from three independent experimentswith five fields per experiment, for a total of 15 fields contributingto the cumulative result.

FIG. 5X3. GRASP55 controls autophagy initiation. (A, B) Effect ofGRASP55 on autophagy induction by measuring LC3-II. BMM cells weretransfected with GRASP55 siRNAs or scramble (Scr) control. At 72 h posttransfection, cells were induced for autophagy, treated or not withBafilomycin A1 (Bat) to inhibit autophagic degradation and LC3-Il/actinratios determined by immunoblotting (A) followed by densitometry (B).Data represent mean values±s.d. (nX3); *Po0.05. (C, D) RAW 264.7 wastransfected with GRASP55 siRNAs or scramble (Scr) siRNA control.Following 48 h of siRNA treatment, cells were transfected withRFP-GFP-LC3 plasmid (GFP is sensitive to acidification, whereas RFP isnot), after 24 h induced for autophagy in EBSS for 1 h and autophagicinduction and flux quantified (graph in D) by determining the number ofearly autophagic organelles (GFP⁻

^(RFP)

^(puncta) and autolysosomal organelles (GFP) ⁺ RFP⁺ puncta) per cell asillustrated in fluorescent images (yellow arrows, GFP⁺ RFP⁺ red arrows,GFP⁻ RFP⁺) Total, yellow+red puncta per cell. Data represent meanvalues±s.d. (nX3); *Po0.05.

FIG. 6X3. HMGB1 is an autophagy-based alternative secretion substrate.(A) Atg^(5fl/fl) Cre⁻ and Atg^(5fl/fl) Cre BMMs, pretreated overnightwith 100 ng/ml LPS, were stimulated for 1 h with 20 mM nigericin (Nig;inflammasome agonist) while incubated in EBSS for induction of autophagyby starvation. Cell culture supernatants were assayed for murine HMGB1by ELISA. Data (normalized to sample with maximum HMGB1 secretion ineach experimental repeat; Cre− and Nig) represent mean values±s.d.(nX3);*Po0.05. (B) LPS-pretreated Atg^(5fl/fl) Cre⁻ and Atg^(5fl/fl)Crep BMMs were stimulated with 20 mM nigericin for 1 h in OptiMEM andthe release of HMGB1 was determined by immunoblotting.

Figure for Example 4

FIG. 1X4. LC3B-II autophagy marker is detected on the surface of cells(see Example 4).

FIG. 2X4 shows that even if the intracellular membranes were to fusewith the plasma membrane (PM), LC3 would not be exposed to the outsideaccording to the current Knowledge. Instead, LC3 would always beshielded from the exposure to the outside and not accessible toantibodies in a sandwich assay, unless the cells were permeabilized.Scheme 1 process B, depicts what is experimentally detected pursuant tothe present invention, i.e. LC3 is exposed on the cell surface on theside of the plasma membrane facing the outside of the cell and thusbeing accessible to the exogenously added antibody to recognize LC3.

Figures for Example 5

Figure IAXS. Depiction of autophagic processes.

FIG. 1BX5. Further depiction of autophagic processes.

FIG. 2X5. Detection of puncta as observed in the experiment of Example5.

FIG. 3X5. High-content imaging experimental design used to examine cellsamples for an autophagy-associated effect on cytoplasmic puncta in theexperiment of Example 5.

FIG. 4X5. Positive and negative controls used in high-content imagingexperiment of Example 5.

FIG. 5X5. Summary of Prestwick and TPIMS screens used in thehigh-content imaging experiment of Example 5.

FIG. 6X5. Comparison of autophagy-associated effects on cytoplasmicpuncta in the experiment of Example 5.

FIG. 7AX5. Prestwick screen data determined in the high-content imagingexperiment of Example 5.

FIG. 8X5. Overlap of hits from two separate Prestwick screens forinduction of autophagy as determined in the experiment of Example 5.

FIG. 9X5. Hits, real and imagined, as determined in the high-contentimaging experiment of Example 5.

FIG. 10X5. Dose response curves to pp242 as determined in thehigh-content imaging experiment of Example 5.

FIG. 11X5. TIPMS library screen conducted in the high-content imagingexperiment of Example 5.

Figures for Example 6

FIG. 1X6. Use of Cellomics ArrayScan to detect induction of authophagy.LC3-RFP/RGP HeLa cells were incubated with the known inducer ofautophagy pp242, anmTOR inhibitor, for 4 hours then fixed in 0.1% PFA.Wells were scanned for number, area, or intensity of GFP+ or RFP+ punctaper cell using a Cellomics ArrayScan. Negative control (DMF-treated)wells were also measured. Each dot represents the data from a singlewell.

FIG. 2X6. Chemical library screen for modulation of autophagy.LC3-RFP/GFP HeLa cells were incubated with compounds from the chemicallibrary for 4 hours, then fixed in 0.1% PFA. Wells were scanned using aCellomics ArrayScan. Negative control (DMSO-treated) and positivecontrol (pp242) wells were also measured. Each dot represents the datafrom a single well.

FIG. 3X6. Shows comparison of replicate chemical library screens formodulation of autophagy. Two different chemical library screens wereperformed as in FIG. 2 on separate days. The data was combined, andcompounds that were hits in both screens were picked for furtherexperimentation.

FIG. 4X6. Dose response measurement of pp242 and induction of autophagy.LC3-RFP/GFP HeLa cells were incubated with different concentrations ofpp242 for 4 hours, then fixed in 0.1% PFA. Wells were scanned using aCellomics ArrayScan. Negative control (DMSO-treated) and positivecontrol (pp242) wells were also measured. Each dot represents the datafrom four separate wells, and error bars are standard deviation.

FIG. 5X6. Overview of chemical screens for modulation of autophagy. Twodifferent chemical library screens were performed on separate days. Thedata was combined, and

compounds that were hits in both screens were picked for furtherexperimentation.

DETAILED DESCRIPTION OF THE INVENTION

It is noted that, as used in this specification and the appended claims,the singular forms “a,” “an,” and “the,” include plural referents unlessexpressly and unequivocally limited to one referent. Thus, for example,reference to “a compound” includes two or more different compound. Asused herein, the term “include” and its grammatical variants areintended to be non-limiting, such that recitation of items in a list isnot to the exclusion of other like items that can be substituted orother items that can be added to the listed items.

The term “compound” or “agent”, as used herein, unless otherwiseindicated, refers to any specific chemical compound disclosed herein andincludes tautomers, regioisomers, geometric isomers as applicable, andalso where applicable, optical isomers (e.g. enantiomers) thereof, aswell as pharmaceutically acceptable salts thereof. Within its use incontext, the term compound generally refers to a single compound, butalso may include other compounds such as stereoisomers, regioisomersand/or optical isomers (including racemic mixtures) as well as specificenantiomers or enantiomerically enriched mixtures of disclosed compoundsas well as diastereomers and epimers, where applicable in context. Theterm also refers, in context to prodrug forms of compounds which havebeen modified to facilitate the administration and delivery of compoundsto a site of activity.

The term “patient” or “subject” is used throughout the specificationwithin context to describe an animal, generally a mammal, including adomesticated mammal including a farm animal (dog, cat, horse, cow, pig,sheep, goat, etc.) and preferably a human, to whom treatment, includingprophylactic treatment (prophylaxis), with the methods and compositionsaccording to the present invention is provided. For treatment of thoseconditions or disease states which are specific for a specific animalsuch as a human patient, the term patient refers to that specificanimal, often a human.

The terms “effective” or “pharmaceutically effective” are used herein,unless otherwise indicated, to describe an amount of a compound orcomposition which, in context, is used to produce or affect an intendedresult, usually the modulation of autophagy within the context of aparticular treatment or alternatively, the effect of a bioactive agentwhich is co administered with the autophagy modulator (autotoxin) in thetreatment of disease.

The terms “treat”, “treating”, and “treatment”, etc., as used herein,refer to any action providing a benefit to a patient at risk for orafflicted by an autophagy mediated disease state or condition asotherwise described herein. The benefit may be in curing the diseasestate or condition, inhibition its progression, or ameliorating,lessening or suppressing one or more symptom of an autophagy mediateddisease state or condition. Treatment, as used herein, encompasses bothprophylactic and therapeutic treatment.

As used herein, the term “autophagy mediated disease state or condition”refers to a disease state or condition that results from disruption inautophagy or cellular self-digestion. Autophagy is a cellular pathwayinvolved in protein and organelle degradation, and has a large number ofconnections to human disease. Autophagic dysfunction is associated withcancer, neurodegeneration, microbial infection and ageing, amongnumerous other disease states and/or conditions. Although autophagyplays a principal role as a protective process for the cell, it alsoplays a role in cell death. Disease states and/or conditions which aremediated through autophagy (which refers to the fact that the diseasestate or condition may manifest itself as a function of the increase ordecrease in autophagy in the patient or subject to be treated andtreatment requires administration of an inhibitor or agonist ofautophagy in the patient or subject) include, for example, cancer,including metastasis of cancer, lysosomal storage diseases (discussedhereinbelow), neurodegeneration (including, for example, Alzheimer'sdisease, Parkinson's disease, Huntington's disease; other ataxias),immune response (T cell maturation, B cell and T cell homeostasis,counters damaging inflammation) and chronic inflammatory diseases (maypromote excessive cytokines when autophagy is defective), including, forexample, inflammatory bowel disease, including Crohn's disease,rheumatoid arthritis, lupus, multiple sclerosis, chronic obstructivepulmony disease/COPD, pulmonary fibrosis, cystic fibrosis, Sjogren'sdisease; hyperglycemic disorders, diabetes (I and II), affecting lipidmetabolism islet function and/or structure, excessive autophagy may leadto pancreatic P-cell death and related hyperglycemic disorders,including severe insulin resistance, hyperinsulinemia, insulin-resistantdiabetes (e.g. Mendenhall's Syndrome, Werner Syndrome, leprechaunism,and lipoatrophic diabetes) and dyslipidemia (e.g. hyperlipidemia asexpressed by obese subjects, elevated low-density lipoprotein (LDL),depressed high-density lipoprotein (HDL), and elevated triglycerides)and metabolic syndrome, liver disease (excessive autophagic removal ofcellular entities-endoplasmic reticulum), renal disease (apoptosis inplaques; glomerular disease), cardiovascular disease (especiallyincluding ischemia, stroke, pressure overload and complications duringreperfusion), muscle degeneration and atrophy, symptoms of aging(including amelioration or the delay in onset or severity or frequencyof aging-related symptoms and chronic conditions including muscleatrophy, frailty, metabolic disorders, low grade inflammation,atherosclerosis and associated conditions such as cardiac andneurological both central and peripheral manifestations includingstroke, age-associated dementia and sporadic form of Alzheimer'sdisease, pre-cancerous states, and psychiatric conditions includingdepression), stroke and spinal cord injury, arteriosclerosis, infectiousdiseases (microbial infections, removes microbes, provides a protectiveinflammatory response to microbial products, limits adapation ofauthophagy of host by microbe for enhancement of microbial growth,regulation of innate immunity) including bacterial, fungal, cellular andviral (including secondary disease states or conditions associated withinfectious diseases), including AIDS and tuberculosis, among others,development (including erythrocyte differentiation),embryogenesis/fertility/infertility (embryo implantation and neonatesurvival after termination of transplacental supply of nutrients,removal of dead cells during programmed cell death) and ageing(increased autophagy leads to the removal of damaged organelles oraggregated macromolecules to increase health and prolong lire, butincreased levels of autophagy in children/young adults may lead tomuscle and organ wasting resulting in ageing/progeria).

The term. “Lysosomal storage disorder” refers to a disease state orcondition that results from a defect in lysosomomal storage. Thesedisease states or conditions generally occur when the lysosomemalfunctions. Lysosomal storage disorders are caused by lysosomaldysfunction usually as a consequence of deficiency of a single enzymerequired for the metabolism of lipids, glycoproteins ormucopolysaccharides. The incidence of lysosomal storage disorder(collectively) occurs at an incidence of about about 1:5,000-1:10,000.The lysosome is commonly referred to as the cell's recycling centerbecause it processes unwanted material into substances that the cell canutilize. Lysosomes break down this unwanted matter via high specializedenzymes. Lysosomal disorders generally are triggered when a particularenzyme exists in too small an amount or is missing altogether. When thishappens, substances accumulate in the cell. In other words, when thelysosome doesn't function normally, excess products destined forbreakdown and recycling are stored in the cell. Lysosomal storagedisorders are genetic diseases, but these may be treated using autophagymodulators (autostatins) as described herein. All of these diseasesshare a common biochemical characteristic, i.e., that all lysosomaldisorders originate from an abnormal accumulation of substances insidethe lysosome. Lysosomal storage diseases mostly affect children whooften die as a consequence at an early stage of life, many within a fewmonths or years of birth. Many other children die of this diseasefollowing years of suffering from various symptoms of their particulardisorder.

Examples of lysosomal storage diseases include, for example, activatordeficiency/GM2 gangliosidosis, alpha-mannosidosis,aspartylglucoaminuria, cholesteryl ester storage disease, chronichexosaminidase A deficiency, cystinosis, Danon disease, Fabry disease,Farber disease, fucosidosis, galactosialidosis, Gaucher Disease (TypesI, H and III), GM! Ganliosidosis, including infantile, lateinfantile/juvenile and adult/chronic), Hunter syndrome (MPS II), I-Celldisease/Mucolipidosis II, Infantile Free Sialic Acid Storage Disease(ISSD), Juvenile Hexosaminidase A Deficiency, Krabbe disease, Lysosomalacid lipase deficiency, Metachromatic Leukodystrophy, Hurler syndrome,Scheie syndrome, Hurler-Scheie syndrome, Sanfilippo syndrome, MorquioType A and B, Maroteaux-Lamy, Sly syndrome, mucolipidosis, multiplesulfate deficiency, Niemann-Pick disease, Neuronal ceroidlipofuscinoses, CLN6 disease, Jansky-Bielschowsky disease, Pompedisease, pycnodysostosis, Sandhoff disease, Schindler disease, Tay-Sachsand Wolman disease, among others.

The term “modulator of autophagy”, “regulator of autophagy” or“autostatin” is used to refer to a compound which functions as anagonist (inducer or up-regulator) or antagonist (inhibitor ordown-regulator) of autophagy. Depending upon the disease state orcondition, autophagy may be upregulated (and require inhibition ofautophagy for therapeutic intervention) or down-regulated (and requireupregulation of autophagy for therapeutic intervention). In mostinstances, in the case of cancer treatment with a modulator of autophagyas otherwise described herein, the autophagy modulator is often anantagonist of autophagy. In the case of cancer, the antagonist(inhibitor) of autophagy may be used alone or combined with an agonistof autophagy

The following compounds have been identified as autophagy modulatorsaccording to the present invention and can be used in the treatment ofan autophagy mediated disease state or condition as otherwise describedherein. It is noted that an inhibitor of autophagy is utilized where thedisease state or condition is mediated through upregulation or anincrease in autophagy which causes the disease state or condition and anagonist of autophagy is utilized where the disease state or condition ismediated through downregulation or a decrease in autophagy. Thefollowing compounds have been identified as autophagy modulators(autotaxins) in autophagy assays according to the present invention:flubendazole, hexachlorophene, propidium iodide, bepridil, clomiphenecitrate (Z,E), GBR 12909, propafenone, metixene, dipivefrin,fluvoxamine, dicyclomine, dimethisoquin, ticlopidine, memantine,bromhexine, norcyclobenzaprine, diperodon and nortriptyline,tetrachlorisophthalonitrile, phenylmercuric acetate and pharmaceuticallyacceptable salts thereof. It is noted that flubendazole,hexachlorophene, propidium iodide, bepridil, clomiphene citrate (Z,E),GBR 12909, propafenone, metixene, dipivefrin, fluvoxamine, dicyclomine,dimethisoquin, ticlopidine, memantine, bromhexine, norcyclobenzaprine,diperodon, nortriptyline and their pharmaceutically acceptable saltsshow activity as agonists or inducers of autophagy in the treatment ofan autophagy-mediated disease, whereas tetrachlorisophthalonitrile,phenylmercuric acetate and their pharmaceutically acceptable salts, finduse as antagonists or inhibitors of autophagy. All of these compoundswill find use as modulators of autophagy in the variousautophagy-mediated disease states and conditions described herein, withthe agonists being preferred in most disease states other than cancer(although inhibitors may also be used alone, or preferably incombination with the agonists) and in the case of the treatment ofcancer, the inhibitors described above are preferred, alone or incombination with an autophagy agonist as described above and/or anadditional anticancer agent as otherwise described herein.

Other compounds which may be used in combination with the autophagymodulators which are described above, include for example, other“additional autophagy modulators” or “additional autostatins” which areknown in the art. These can be combined with one or more of theautophagy modulators which are disclosed above to provide novelpharmaceutical compositions and/or methods of treating autophagymediated disease states and conditions which are otherwise describedherein. These additional autophagy modulators including benzethonium,niclosamide, monensin, bromperidol, levobunolol, dehydroisoandosterone3-acetate, sertraline, tamoxifen, reserpine, hexachlorophene,dipyridamole, harmaline, prazosin, lidoflazine, thiethylperazine,dextromethorphan, desipramine, mebendazole, canrenone, chlorprothixene,maprotiline, homochlorcyclizine, loperamide, nicardipine,dexfenfluramine, nilvadipine, dosulepin, biperiden, denatonium,etomidate, toremifene, tomoxetine, clorgyline, zotepine, beta-escin,tridihexethyl, ceftazidime, methoxy-6-harmalan, melengestrol,albendazole, rimantadine, chlorpromazine, pergolide, cloperastine,prednicarbate, haloperidol, clotrimazole, nitrofural, iopanoic acid,naftopidil, Methimazole, Trimeprazine, Ethoxyquin, Clocortolone,Doxycycline, Pirlindole mesylate, Doxazosin, Deptropine, Nocodazole,Scopolamine, Oxybenzone, Halcinonide, Oxybutynin, Miconazole,Clomipramine, Cyproheptadine, Doxepin, Dyclonine, Salbutamol, Flavoxate,Amoxapine, Fenofibrate, Pimethixene and mixtures thereof.

The term “co-administration” or “combination therapy” is used todescribe a therapy in which at least two active compounds in effectiveamounts are used to treat an autophagy mediated disease state orcondition as otherwise described herein, either at the same time orwithin dosing or administration schedules defined further herein orascertainable by those of ordinary skill in the art. Although the termco-administration preferably includes the administration of two activecompounds to the patient at the same time, it is not necessary that thecompounds be administered to the patient at the same time, althougheffective amounts of the individual compounds will be present in thepatient at the same time. In addition, in certain embodiments,co-administration will refer to the fact that two compounds areadministered at significantly different times, but the effects of thetwo compounds are present at the same time. Thus, the termco-administration includes an administration in which one active agent(especially an autophagy modulator) is administered at approximately thesame time (contemporaneously), or from about one to several minutes toabout 24 hours or more than the other bioactive agent coadministeredwith the autophagy modulator. The additional bioactive agent may be anybioactive agent, but is generally selected from an additional autophagymediated compound, an additional anticancer agent, or another agent,such as a mTOR inhibitor such as pp242, rapamycin, envirolimus,everolimus or cidaforollimus, among others including epigallocatechingallate. (EGCG), caffeine, curcumin or reseveratrol (which mTORinhibitors find particular use as enhancers of autophagy using thecompounds disclosed herein and in addition, in the treatment of cancerwith an autophagy modulator (inhibitor) as described herein, includingin combination with tetrachlorisophthalonitrile, phenylmercuric acetateand their pharmaceutically acceptable salts, which are inhibitors ofautophagy. It is noted that in the case of the treatment of cancer, theuse of an autophagy inhibitor is preferred, alone or in combination withan autophagy inducer (agonist) as otherwise described herein and/or amTOR inhibitor as described above. In certain embodiments, an mTORinhibitor selected from the group consisting of pp242, rapamycin,envirolimus, everolimus, cidaforollimus, epigallocatechin gallate(EGCG), caffeine, curcumin, reseveratrol and mixtures thereof may becombined with at least one agent selected from the group consisting ofdigoxin, xylazine, hexetidine and sertindole, the combination of suchagents being effective as autophagy modulators in combination.

The term “cancer” is used throughout the specification to refer to thepathological process that results in the formation and growth of acancerous or malignant neoplasm, i.e., abnormal tissue that grows bycellular proliferation, often more rapidly than normal and continues togrow after the stimuli that initiated the new growth cease. Malignantneoplasms show partial or complete lack of structural organization andfunctional coordination with the normal tissue and most invadesurrounding tissues, metastasize to several sites, and are likely torecur after attempted removal and to cause the death of the patientunless adequately treated.

As used herein, the term neoplasia is used to describe all cancerousdisease states and embraces or encompasses the pathological processassociated with malignant hematogenous, ascitic and solid tumors.Representative cancers include, for example, stomach, colon, rectal,liver, pancreatic, lung, breast, cervix uteri, corpus uteri, ovary,prostate, testis, bladder, renal, brain/CNS, head and neck, throat,Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma, leukemia,melanoma, non-melanoma skin cancer (especially basal cell carcinoma orsquamous cell carcinoma), acute lymphocytic leukemia, acute myelogenousleukemia, Ewing's sarcoma, small cell lung cancer, choriocarcinoma,rhabdomyosarcoma, Wilms' tumor, neuroblastoma, hairy cell leukemia,mouth/pharynx, oesophagus, larynx, kidney cancer and lymphoma, amongothers, which may be treated by one or more compounds according to thepresent invention. In certain aspects, the cancer which is treated islung cancer, breast cancer, ovarian cancer and/or prostate cancer.

The term “tumor” is used to describe a malignant or benign growth ortumefacent.

The term “additional anti-cancer compound”, “additional anti-cancerdrug” or “additional anti-cancer agent” is used to describe any compound(including its derivatives) which may be used to treat cancer. The“additional anti-cancer compound”, “additional anti-cancer drug” or“additional anti-cancer agent” can be an anticancer agent which isdistinguishable from a CIAE-inducing anticancer ingredient such as ataxane, vinca alkaloid and/or radiation sensitizing agent otherwise usedas chemotherapy/cancer therapy agents herein. In many instances, theco-administration of another anti-cancer compound according to thepresent invention results in a synergistic anti-cancer effect. Exemplaryanti-cancer compounds for co-administration with formulations accordingto the present invention include anti-metabolites agents which arebroadly characterized as antimetabolites, inhibitors of topoisomerase Iand II, alkylating agents and microtubule inhibitors (e.g., taxol), aswell as tyrosine kinase inhibitors (e.g., surafenib), EGF kinaseinhibitors (e.g., tarceva or erlotinib) and tyrosine kinase inhibitorsor ABL kinase inhibitors (e.g. imatinib).

Anti-cancer compounds for co-administration include, for example,Aldesleukin; Alemtuzumab; alitretinoin; allopurinol; altretamine;amifostine; anastrozole; arsenic trioxide; Asparaginase; BCG Live;bexarotene capsules; bexarotene gel; bleomycin; busulfan intravenous;busulfan oral; calusterone; capecitabine; carboplatin; carmustine;carmustine with Polifeprosan 20 Implant; celecoxib; chlorambucil;cisplatin; cladribine; cyclophosphamide; cytarabine; cytarabineliposomal; dacarbazine; dactinomycin; actinomycin D; Darbepoetin alfa;daunorubicin liposomal; daunorubicin, daunomycin; Denileukin diftitox,dexrazoxane; docetaxel; doxorubicin; doxorubicin liposomal;Dromostanolone propionate; Elliott's B Solution; epirubicin; Epoetinalfa estramustine; etoposide phosphate; etoposide (VP-16); exemestane;Filgrastim; floxuridine (intraarterial); fludarabine; fluorouracil(5-FU); fulvestrant; gemtuzumab ozogamicin; gleevec (imatinib);goserelin acetate; hydroxyurea; Ibritumomab Tiuxetan; idarubicin;ifosfamide; imatinib mesylate; Interferon alfa-2a; Interferon alfa-2b;irinotecan; letrozole; leucovorin; levamisole; lomustine (CCNU);meclorethamine (nitrogen mustard); megestrol acetate; melphalan (L-PAM);mercaptopurine (6-MP); mesna; methotrexate; methoxsalen; mitomycin C;mitotane; mitoxantrone; nandrolone phenpropionate; Nofetumomab; LOddC;Oprelvekin; oxaliplatin; paclitaxel; pamidronate; pegademase;Pegaspargase; Pegfilgrastim; pentostatin; pipobroman; plicamycin;mithramycin; porfimer sodium; procarbazine; quinacrine; Rasburicase;Rituximab; Sargramostim; streptozocin; surafenib; talbuvidine (LDT);talc; tamoxifen; tarceva (erlotinib); temozolomide; teniposide (VM-26);testolactone; thioguanine (6-TG); thiotepa; topotecan; toremifene;Tositumomab; Trastuzumab; tretinoin (ATRA); Uracil Mustard; valrubicin;valtorcitabine (monoval LDC); vinblastine; vinorelbine; zoledronate; andmixtures thereof, among others.

Co-administration of one of the formulations of the invention withanother anticancer agent will often result in a synergistic enhancementof the anticancer activity of the other anticancer agent, an unexpectedresult. One or more of the present formulations comprising an autophagymodulator (autostatin) may also be co-administered with anotherbioactive, agent (e.g., antiviral agent, antihyperproliferative diseaseagent, agents which treat chronic inflammatory disease, among others asotherwise described herein).

The term “antiviral agent” refers to an agent which may be used incombination with authophagy modulators (autostatins) as otherwisedescribed herein to treat viral infections, especially including HIVinfections, HBV infections and/or HCV infections. Exemplary anti-HIVagents include, for example, nucleoside reverse transcriptase inhibitors(NRTI), non-nucleoside reverse transcriptase inhibitors (NNRTI),protease inhibitors, fusion inhibitors, among others, exemplarycompounds of which may include, for example, 3TC (Lamivudine), AZT(Zidovudine), (−)-FTC, ddl (Didanosine), ddC (zalcitabine), abacavir(ABC), tenofovir (PMPA), D-D4FC (Reverset), D4T (Stavudine), Racivir,L-FddC, L-FD4C, NVP (Nevirapine), DLV (Delavirdine), EFV (Efavirenz),SQVM (Saquinavir mesylate), RTV (Ritonavir), IDV (Indinavir), SQV(Saquinavir), NFV (Nelfinavir), APV (Amprenavir), LPV (Lopinavir),fusion inhibitors such as T20, among others, fuseon and mixturesthereof, including anti-HIV compounds presently in clinical trials or indevelopment. Exemplary anti-HBV agents include, for example, hepsera(adefovir dipivoxil), lamivud ine, entecavir, telbivudine, tenofovir,emtricitabine, clevud ine, valtoricitabine, amdoxovir, pradefovir,racivir, BAM 205, nitazoxanide, UT 231-B, Bay 41-4109, EHT899, zadaxin(thymosin alpha-I) and mixtures thereof. Anti-HCV agents include, forexample, interferon, pegylated intergeron, ribavirin, NM 283, VX-950(telaprevir), SCH 50304, TMC435, VX-500, BX-813, SCHSO3034, R1626,ITMN-191 (R7227), R7128, PF-868554, TT033, CGH-759, GI 5005, MK-7009,SIRNA-034, MK-0608, A-837093, GS 9190, ACH-1095, GSK625433, TG4040(MVA-HCV), A-831, F351, NS5A, NS4B, ANA598, A-689, GNI-104, IDX102,ADX184, GL59728, GL60667, PSI-7851, TLR9 Agonist, PHX1 766, SP-30 andmixtures thereof.

As used herein, “antibody” includes, but is not limited to, monoclonalantibodies. The following disclosure from U.S. Patent ApplicationDocument No. 20100284921, the entire contents of which are herebyincorporated by reference, exemplifies techniques that are useful inmaking antibodies employed in formulations of the instant invention.

As described in U.S. Patent Application Document No. 20100284921,“antibodies . . . may be polyclonal or monoclonal. Monoclonal antibodiesare preferred. The antibody is preferably a chimeric antibody. For humanuse, the antibody is preferably a humanized chimeric antibody.

An anti-target-structure antibody . . . may be monovalent, divalent orpolyvalent in order to achieve target structure binding. Monovalentimmunoglobulins are dimers (HL) formed of a hybrid heavy chainassociated through disulfide bridges with a hybrid light chain. Divalentimmunoglobulins are tetramers (H2L2) formed of two dimers associatedthrough at least one disulfide bridge.

The invention also includes [use of] functional equivalents of theantibodies described herein. Functional equivalents have bindingcharacteristics comparable to those of the antibodies, and include, forexample, hybridized and single chain antibodies, as well as fragmentsthereof. Methods of producing such functional equivalents are disclosedin PCT Application Nos. WO 1993/21319 and WO 1989/09622. Functionalequivalents include polypeptides with amino acid sequences substantiallythe same as the amino acid sequence of the variable or hypervariableregions of the antibodies raised against target integrins according tothe practice of the present invention.

Functional equivalents of the anti-target-structure antibodies furtherinclude fragments of antibodies that have the same, or substantially thesame, binding characteristics to those of the whole antibody. Suchfragments may contain one or both Fab fragments or the F(ab′).sub.2fragment. Preferably the antibody fragments contain all six complementdetermining regions of the whole antibody, although fragments containingfewer than all of such regions, such as three, four or five complementdetermining regions, are also functional. The functional equivalents aremembers of the IgG immunoglobulin class and subclasses thereof, but maybe or may combine any one of the following immunoglobulin classes: 1gM,1gA, 1gD, or IgE, and subclasses thereof. Heavy chains of varioussubclasses, such as the IgG subclasses, are responsible for differenteffector functions and thus, by choosing the desired heavy chainconstant region, hybrid antibodies with desired effector function areproduced. Preferred constant regions are gamma 1 (IgG 1), gamma 2 (IgG2and IgG), gamma 3 (IgG3) and gamma 4 (IgG4). The light chain constantregion can be of the kappa or lambda type.

The monoclonal antibodies may be advantageously cleaved by proteolyticenzymes to generate fragments retaining the target structure bindingsite. For example, proteolytic treatment of IgG antibodies with papainat neutral pH generates two identical so-called “Fab” fragments, eachcontaining one intact light chain disulfide-bonded to a fragment of theheavy chain (Fe). Each Fab fragment contains one antigen-combining site.The remaining portion of the IgG molecule is a dimer known as “Fe”.Similarly, pepsin cleavage at pH 4 results in the so-called F(ab′)2fragment.

Single chain antibodies or Fv fragments are polypeptides that consist ofthe variable region of the heavy chain of the antibody linked to thevariable region of the light chain, with or without an interconnectinglinker. Thus, the Fv comprises an antibody combining site.

Hybrid antibodies may be employed. Hybrid antibodies have constantregions derived substantially or exclusively from human antibodyconstant regions and variable regions derived substantially orexclusively from the sequence of the variable region of a monoclonalantibody from each stable hybridoma.

Methods for preparation of fragments of antibodies (e.g. for preparingan antibody or an antigen binding fragment thereof having specificbinding affinity for either caspase-1 or an autophagy-relatedimmunomodulatory cytokine) are either described in the experimentsherein or are otherwise known to those skilled in the art. See, Goding,“Monoclonal Antibodies Principles and Practice”, Academic Press (1983),p. 119-123. Fragments of the monoclonal antibodies containing theantigen binding site, such as Fab and F(ab′)2 fragments, may bepreferred in therapeutic applications, owing to their reducedimmunogenicity. Such fragments are less immunogenic than the intactantibody, which contains the immunogenic Fe portion. Hence, as usedherein, the term “antibody” includes intact antibody molecules andfragments thereof that retain antigen binding ability.

When the antibody used in the practice of the invention is a polyclonalantibody (IgG), the antibody is generated by inoculating a suitableanimal with a target structure or a fragment thereof. Antibodiesproduced in the inoculated animal that specifically bind the targetstructure are then isolated from fluid obtained from the animal.Anti-target-structure antibodies may be generated in this manner inseveral non-human mammals such as, but not limited to, goat, sheep,horse, rabbit, and donkey. Methods for generating polyclonal antibodiesare well known in the art and are described, for example in Harlow etal. (In: Antibodies, A Laboratory Manual, 1988, Cold Spring Harbor,N.Y.).

When the antibody used in the methods used in the practice of theinvention is a monoclonal antibody, the antibody is generated using anywell known monoclonal antibody preparation procedures such as thosedescribed, for example, in Harlow et al. {supra) and in Tuszynski et al.(Blood 1988, 72:109-115). Generally, monoclonal antibodies directedagainst a desired antigen are generated from mice immunized with theantigen using standard procedures as referenced herein. Monoclonalantibodies directed against full length or fragments of target structuremay be prepared using the techniques described in Harlow et al. (supra).

The effects of sensitization in the therapeutic use of animal-originmonoclonal antibodies in the treatment of human disease may bediminished by employing a hybrid molecule generated from the same Fabfragment, but a different Fe fragment, than contained in monoclonalantibodies previously administered to the same subject. It iscontemplated that such hybrid molecules formed from theanti-target-structure monoclonal antibodies may be used in the presentinvention. The effects of sensitization are further diminished bypreparing animal/human chimeric antibodies, e.g., mouse/human chimericantibodies, or humanized (i.e. CDR-grafted) antibodies. Such monoclonalantibodies comprise a variable region, i.e., antigen binding region, anda constant region derived from different species. By ‘chimeric’ antibodyis meant an antibody that comprises elements partly derived from onespecies and partly derived form at least one other species, e.g., amouse/human chimeric antibody.

Chimeric animal-human monoclonal antibodies may be prepared byconventional recombinant DNA and gene transfection techniques well knownin the art. The variable region genes of a mouse antibody-producingmyeloma cell line of known antigen-binding specificity are joined withhuman immunoglobulin constant region genes. When such gene constructsare transfected into mouse myeloma cells, the antibodies produced arelargely human but contain antigen-binding specificities generated inmice. As demonstrated by Morrison et al., 1984, Proc. Natl. Acad. Sci.USA 81:6851-6855, both chimeric heavy chain V region exon (VH)-humanheavy chain C region genes and chimeric mouse light chain V region exon(VK)-human K light chain gene constructs may be expressed whentransfected into mouse myeloma cell lines. When both chimeric heavy andlight chain genes are transfected into the same myeloma cell, an intactH2L2 chimeric antibody is produced. The methodology for producing suchchimeric antibodies by combining genomic clones of V and C region genesis described in the above-mentioned paper of Morrison et al., and byBoulianne et al. (Nature 1984, 312:642-646). Also see Tan et al. (J.Immunol. 1985, 135:3564-3567) for a description of high level expressionfrom a human heavy chain promotor of a human-mouse chimeric K chainafter transfection of mouse myeloma cells. As an alternative tocombining genomic DNA, cDNA clones of the relevant V and C regions maybe combined for production of chimeric antibodies, as described byWhitte et al. (Protein Eng. 1987, 1:499-505) and Liu et al. (Proc. Natl.Acad. Sci. USA 1987, 84:3439-3443). For examples of the preparation ofchimeric antibodies, see the following U.S. Pat. Nos. 5,292,867;5,091,313; 5,204,244; 5,202,238; and 5,169,939. The entire disclosuresof these patents, and the publications mentioned in the precedingparagraph, are incorporated herein by reference. Any of theserecombinant techniques are available for production of rodent/humanchimeric monoclonal antibodies against target structures.

To further reduce the immunogenicity of murine antibodies, “humanized”antibodies have been constructed in which only the minimum necessaryparts of the mouse antibody, the complementarity-determining regions(CDRs), are combined with human V region frameworks and human C regions(Jones et al., 1986, Nature 321:522-525; Verhoeyen et al., 1988, Science239:1534-1536; Hale et al., 1988, Lancet 2:1394-1399; Queen et al.,1989, Proc. Natl. Acad. Sci. USA 86:10029-10033). The entire disclosuresof the aforementioned papers are incorporated herein by reference. Thistechnique results in the reduction of the xenogeneic elements in thehumanized antibody to a minimum. Rodent antigen binding sites are builtdirectly into human antibodies by transplanting only the antigen bindingsite, rather than the entire variable domain, from a rodent antibody.This technique is available for production of chimeric rodent/humananti-target structure antibodies of reduced human immunogenicity.”

Further, standard techniques for growing cells, separating cells, andwhere relevant, cloning, DNA isolation, amplification and purification,for enzymatic reactions involving DNA ligase, DNA polymerase,restriction endonucleases and the like, and various separationtechniques are those known and commonly employed by those skilled in theart. A number of standard techniques are described in Sambrook et al.,1989 Molecular Cloning, Second Edition, Cold Spring Harbor Laboratory,Plainview, N.Y.; Maniatis et al., 1982 Molecular Cloning, Cold SpringHarbor Laboratory, Plainview, N.Y.; Wu (Ed.) 1993 Meth. Enzymol. 218,Part I; Wu (Ed.) 1979 Meth. Enzymol. 68; Wu et al., (Eds.) 1983 Meth.Enzymol. 100 and 101; Grossman and Moldave (Eds.) 1980 Meth. Enzymol.65; Miller (ed.) 1972 Experiments in Molecular Genetics, Cold SpringHarbor Laboratory, Cold Spring Harbor; New York; Old and Primrose, 1981Principles of Gene Manipulation, University of California Press,Berkeley; Schleif and Wensink, 1982 Practical Methods in MolecularBiology; Glover (Ed.) 1985 DNA Cloning Vol. I and II, IRL Press, Oxford,UK; Hames and Higgins (Eds.) 1985 Nucleic Acid Hybridization, IRL Press,Oxford, UK; and Setlow and Hollaender 1979 Genetic Engineering:Principles and Methods, Vols. 1-4, Plenum Press, New York. Abbreviationsand nomenclature, where employed, are deemed standard in the field andcommonly used in professional journals such as those cited herein.

High-content imaging techniques and diagnostic methods described hereincan use fluorescence-inducing compounds, e.g. a fluorescent moiety suchas a fluorescein dye or a rhodamine dye. In some embodiments, thefluorescent moiety comprises two or more fluorescent dyes that can actcooperatively with one another, for example by fluorescence resonanceenergy transfer (“FRET”). The fluorescent moiety may be any fluorophorethat is capable of producing a detectable fluorescence signal in anassay medium; the fluorescence signal can be “self-quenched” and capableof fluorescing in an aqueous medium. “Quench” refers to a reduction inthe fluorescence intensity of a fluorescent group as measured at aspecified wavelength, regardless of the mechanism by which the reductionis achieved. As specific examples, the quenching may be due to molecularcollision, energy transfer such as FRET, a change in the fluorescencespectrum (color) of the fluorescent group or any other mechanism. Theamount of the reduction is not critical and may vary over a broad range.The only requirement is that the reduction be measurable by thedetection system being used. Thus, a fluorescence signal is “quenched”if its intensity at a specified wavelength is reduced by any measurableamount.

Examples of fluorophores include xanthenes such as fluoresceins,rhodamines and rhodols, cyanines, phtalocyanines, squairanines, bodipydyes, pyrene, anthracene, naphthalene, acridine, stilbene, indole orbenzindole, oxazole or benzoxazole, thiazole or benzothiazole,carbocyanine, carbostyryl, prophyrin, salicylate, anthranilate, azulene,perylene, pyridine, quinoline, borapolyazaindacene, xanthene, oxazine orbenzoxazine, carbazine, phenalenone, coumarin, benzofuran, orbenzphenalenone. Examples of rhodamine dyes include, but are not limitedto, rhodamine B, 5-carboxyrhodamine, rhodamine X (ROX),4,7-dichlororhodamine X (dROX), rhodamine 6G (R6G),4,7-dichlororhodamine 6G, rhodamine 110 (R1 10), 4,7-dichlororhodamine110 (dR1 10), tetramethyl rhodamine (TAMRA) and4,7-dichlorotetramethylrhodamine (dTAMRA).

Examples of fluorescein dyes include, but are not limited to,4,7-dichlorofluoresceins, 5-carboxyfluorescein (5-FAM) and6-carboxyfluorescein (6-FAM).

For example, cells can be transfected with green fluorescentprotein-tagged autophagic marker protein light chain 3 (GFP-LC3) (seee.g., Gonzalez-Polo R-A, et al. (2005) J. Cell Sci. 118:3091-3102),which is a fluorescent fusion protein that is incorporated intoautophagosomes (also called autophagic vesicles, or AV); confocalmicroscopy can be used to score the number of autophagosomes (LC3-GFPdots) per cell. Although this can be done using robotics and automatedmicroscopy

Detection and spatial localization in a biological sample as describedherein may be based on, but not restricted to fluorescence in theultra-violet, visible, infrared spectral regions, or may report viaradiofrequencies (MRI/NMR) and well as radioactive detection. Inaddition, a reporter group containing heavy atoms is employed fordetection using electron microscopy (EM or TEM), scanning EM (SEM) ormass spectral or equivalent techniques. In alternative embodiments, thereporter (domains or moieties) comprise functional groups that eitherturn off or on its reporting function from its native state, but in thepresence of a biological sample (for example; pH change, presence of aspecific enzyme, metal etc.) changes its state, giving further detailsto the biological environment in an autophagic vesicle.

In one embodiment of the invention, “sandwich” type immunoassays areutilized to measure LC3 in a sample, preferably a blood sample, tofacilitate an ease of analysis of LC3 activity in the blood of a patientor subject. In one embodiment, the methods of the invention utilize acapture antibody that specifically binds to LC3. The capture antibodymay be coupled to a solid substrate or solid phase. Examples of suitablesubstrates include, but are not limited to, wells of microliter platesor cuvettes, or nitrocellulose or nylon membranes. In one embodiment ofthe invention, the capture antibodies are coupled to paramagneticparticles in wells of microtiter plates or cuvettes. Far example,biotin-coupled capture antibodies can couple to streptavidin coatedparamagnetic particles via the well known avidin-biotin bindingreaction. Other methods of coupling the capture antibody to the solidphase of the assays are known to those skilled in the art. LC3antibodies, including monoclonal antibodies are available in the art(available from Cell Signalling Technology, Danvers, Massachussetts,USA). The use of these and/or other antibodies which are otherwisedescribed herein or are well known in the art and may be readily adaptedto the present invention.

In practicing the sandwich immunoassay, LC3 may also be exposed to adetection antibody that is coupled to a detectable label. Examples ofsuitable labels are described above, one example of a label is anacridinium ester. Methods of coupling labels to antibodies are wellknown in the art. For example, acridinium, as a “sulfonyl chlorideester” can be crosslinked to the detection antibody by the reaction ofthe lysly moiety of the epsilon amino group of lysine in proteins, suchas antibodies, to the acridinium ester. The reaction products may thenbe separated by size exclusion chromatography on Sepharose beads orotherwise.

In certain embodiments of the invention, the sandwich immunoassays maybe chemiluminescent immunoassays, but colorimetric assays may bepreferred for point of care applications, including home applications.Although specific monoclonal antibodies are disclosed herein and arecommercially available, other monoclonal antibodies that could be usedas capture and detection antibodies for LC3 as described herein can beproduced using conventional methods known in the art. See, for example,Kohler and Milstein, (1975) Nature, 256:495-97; or Sambrook et al.(2001) Molecular Cloning: A Laboratory Manual, 3rd edition, Cold SpringHarbor Laboratory Press. Briefly, animals, such as mice, are injectedwith an antigen, such as LC3 or fragments thereof, that may be coupledto a carrier protein. The animals are boosted with one or more antigeninjections, and are hyperimmunized by an intravenous (IV) booster aboutthree days before fusion. Spleen cells from the mice are isolated andare fused by standard methods to myeloma cells. Hybridomas are selectedin standard hypoxanthine/aminopterin/thymine (HAT) medium, according tostandard methods. Hybridomas secreting antibodies which recognizedifferent epitopes of the antigen are identified, cultured, andsubcloned using standard immunological techniques. The antibodies arethen screened for the desired specificity or cross reactivity usingmethods known in the art.

Although one embodiment of the invention employs calorimetric orchemiluminescent sandwich inumunoassays to practice the methods of theinvention, other immunoassays, such as ELISAs and RIAs may be used. Theparameters and components of the assays are determined and optimized asis well known to those skilled in the art such that the assays providemeasurement of LC3 levels in the biological samples being assayed. Inaddition, although certain embodiments of the invention utilizeantibodies as the agents capturing LC3, LC3 may be captured in theassays of the invention using other chemical agents or molecules thatare not antibodies. For example, such an agent may recognizecarbohydrate profiles of LC3 and thereby bind the LC3 to a solid phasein a similar manner as the capture antibodies described herein.

In some embodiments of the invention, it may be desirable to automatethe methods as much as practical in order to improve replicability ofthe results and reduce the time and costs required to conduct theassays. Automated assays used to practice the methods of the inventionpermit users to conduct at least about 80 tests per hour, and preferablymore than about 100 test per hour.

One may also use any conventional, non-automated, assay device topractice the methods of the invention. For example, a conventionalmicrotiter plate can be used to store the various solutions used inperforming the assay. The device should permit the biological sample tobe exposed to a combination of antibodies. The antibodies may recognizedifferent epitopes of the antigen(s) being assayed. The device shouldalso cause the bound antigen to be retained to a substrate as solutionsare added and removed during the assay.

By way of example, and not by way of limitation, wells of a microtiterplate can be loaded with a solution containing streptavidin coatedmagnetic particles, as described herein. A solution containing biotincoupled capture antibodies (e.g., biotin coupled mAb) is added to thewell to enable the coupling of the capture antibodies to the magneticparticles. A concentration of capture antibody is empirically selected(based on expected antigen concentrations) as discussed herein, topermit binding of all, or essentially all, of the test antigen that isavailable in the sample. In that regard, typical antigen concentrationsin biological samples are in the nanogram to low microgram range (e.g.less than 1 ng/ml-5 μg/ml) so that the capture antibody concentrationsare in the low to high microgram range (e.g. 1-100 μg/ml). The sample isadded to the well. If the sample contains the antigens of interest(e.g., LC3), the antigen will bind to the capture antibodies. The plateis exposed to a magnetic field to immobilize the magnetic particles, andthe solution is removed from the well; but the antigen will not beremoved because it is bound to the antibodies that are bound to themagnetic particles that are immobilized by the magnetic field. Asolution containing the detection antibody coupled to a label (e.g.,acridinium labeled mAb) is added to the well containing the boundantigen. As indicated elsewhere herein, the concentration of thedetection antibody is preferably selected so that all, or essentiallyall, of the test antigen molecules (e.g., LC3) are bound by thedetection antibody. Thus, the detection antibody can be provided atconcentrations at least an order of magnitude greater than the expectedconcentration of the test antigen. For example, if a test antigen has anexpected concentration of 2 ng/ml, the detection antibody concentrationcan be at least 20 ng/ml (0.02 μg/ml). After a sufficient amount of time(from about 10 minutes to about 8 or more hours, which is determined ina calibration step), determined and optimized empirically as describedherein, the plate is exposed to a magnetic field, the solution is thenremoved, and the sample is washed. The amount of label remaining in thewell is then measured (e.g., by a luminometer). The measured values canbe quantitative or qualitative. Quantitative results are usuallypreferred. The measured values may then be compared to a standard or athreshold.

One immunoassay system which may be used in the present invention is theNichols Advantage® immunoassay system, which is a fully automatedchemiluminescent system. The system is a bench-top instrument thatperforms solid phase chemiluminescent immunoassays. Streptavidin-coatedmagnetic particles and biotinylated antibodies may be employed in theassay system. Acridinium ester is typically the chemiluminescence labelfor signal detection. Other assay systems may also be employed in thepresent method.

In practicing the methods of the invention, a control may be provided inthe assay to ensure that the reactions have been successful. Forexample, a control could be provided with a polyclonal antibody solutionfor other analytes present in the biological sample or the same analytespresent in other control samples.

In point of care applications, and in home assay tests, the followingexemplary colorimetric assay may be used. The assay may also bechemiluminescent, but is preferably colorimetric in nature (for ease ofuse). The test device for determining concentration levels of LC3 may bea nitrocellulose-based (or other appropriate polymeric material)colorimetric sandwich assay (nitrocellulose-based sandwich assay) or twoantibody test based upon a capture antibody and a detection antibody (atleast one) wherein the capture and detection antibodies recognize andbind different epitopes of LC3, and wherein one of the antibodies (thedetection antibody) is coupled to a label that produces a detectable orcolorimetric signal (through a dye such as a gold-based dye) and theother antibody, the capture antibody, is anchored to a support,preferably a polymeric material, preferably a nitrocellulose or otherfilm layer, wherein the capture antibody is fixed in a line in the filmlayer. In this preferred assay, both the capture antibody and thedetection antibody are specific for different epitopes on LC3, such thatthe LC3 may be measured. In preferred aspects, the capture antibody isspecific for a particular epitope on LC3 and the detection antibody maybe much less specific provided that the antibody binds, and consequentlylabels, essentially all of the LC3 which is bound to the captureantibody. In this assay the capture antibody is specific for a differentepitope on LC3 than is the detection antibody although both the captureand detection antibodies (in the case of the detection antibody, eithersingly or collectively) are specific for LC3 to maximize accuracy.

In this point of home or point of care diagnostic test, the detectionantibody is linked to dye (gold-based or other) and initially is in anupper layer material which is porous to liquid and is free to move to alower layer when it comes into contact with liquid, such as blood,serum, plasma or urine, which contains LC3. The detection antibody ofthe upper layer is free to move from the upper layer (preferably aporous sponge material) to the lower layer. The other antibody (thecapture antibody) is anchored in the nitrocellose matrix or othersimilar material in a shape like a line. The LC3 containing cells inserum would enter the device and bind to the antibody-dye. There can anopening in the device case called the “result window”, exposing anycolor from the dye. The LC3 antibody-dye would then move into or throughthe nitrocellulose matrix until it reaches the anchored capturedantibody. The result (“result line”) would be a colored line in the“result window”. A further line of die could be shown in the “resultwindow”. This is the “control dye line” or line generated by a dye thatcorresponds to the color and intensity that would be observed in theline in the “result window” from the antibody-dye: LC3: anchoredantibody sandwich if blood/serum/urine concentration was formed by atleast about a certain concentration of LC3 containing cells. If the“result line” was not as intense as the “control dye line” then LC3 areat which evidence that autophagy was not responsible for the patient'sillness or condition. If the “result line” was similar or more intensethan the “control dye line” then the patient is predicted to have anautophagy-mediated disease state and/or condition with a high accuracy.The aim would be for a test of high sensitivity calibrated preferably toa level of LC3 predictive of a disease state.

“Cells implicated in a lipid-related metabolic disorder” include anycell manifesting a disruption of cellular lipid homeostasis. Forexample, familial hypercholesterolemia (FH) is caused by mutations inthe LDL receptor. Although LDL receptors are expressed ubiquitously, thehepatic LDL receptor has the greatest quantitative effect in controllingplasma LDL levels. Hence hepatocytes are type of cells implicated in alipid-related metabolic disorder. Lipoprotein lipase (LPL) deficiency isa rare autosomal recessive disorder characterized by markedly elevatedplasma levels of triglycerides. Most LPL expression is in muscle andadipose tissue. Muscle (e.g. skeletal muscle) and adipose tissue cellsare therefore another type of useful cell implicated in metabolicdisorders. ApoE serves as a ligand that mediates the clearance ofchylomicron and VLDL remnant lipoproteins by binding to the LDL receptorand related members of the same gene family. Most apoE in plasma isderived from the liver. A genetic deficiency of apoE results insubstantially elevated levels of lipoprotein remnants and is associatedwith an increased risk for atherosclerotic vascular disease. Hepatocytescan be used in the evaluation of this disorder using techniquesdescribed herein.

Unesterified cholesterol is esterified to cholesteryl ester in the bloodby the lipoprotein-associated enzyme lecithin: cholesterolacyltransferase (LCAT). Complete LCAT deficiency is is characterized bymarkedly reduced HDL cholesterol levels (less than 10 mg/dl), cornealopacities, anemia, and progressive proteinuria and renal insufficiencyeventually leading to end-stage renal disease. Although LCAT is normallysynthesized in the liver, because it is a secreted protein it couldtheoretically be made in other tissues such as muscle. Hepatocytes andmuscle cells can therefore be used in the evaluation of this disorderusing techniques described herein. Tangier disease is a rare geneticdisorder associated with markedly reduced HDL cholesterol levels (lessthan 5 mg/dl), the accumulation of cholesterol in macrophages andrelated cells, neuropathy, and premature atherosclerosis. Macrophages orbone marrow stem cells can therefore be used in the evaluation of thisdisorder using techniques described herein. ApoA-I is the major proteinin HDL; a genetic deficiency of apoA-I results in markedly reduced HDLand seems, at least in some kindreds, to increase the risk for coronaryartery disease. Hepatocytes and muscle cells can be used in theevaluation of this disorder using techniques described herein.

Cell samples used in methods of the invention can be stem cells. Stemcells are cells capable of differentiation into other cell types,including those having a particular, specialized function (i.e.,terminally differentiated cells, such as erythrocytes, macrophages,etc.), progenitor (i.e., “multipotent”) cells which can give rise to anyone of several different terminally differentiated cell types, and cellsthat are capable of giving rise to various progenitor cells. Cells thatgive rise to some or many, but not all, of the cell types of an organismare often termed “pluripotent” stem cells, which are able todifferentiate into any cell type in the body of a mature organism,although without reprogramming they are unable to de-differentiate intothe cells from which they were derived. “Multipotent” stem/progenitorcells (e.g., neural stem cells) have a more narrow differentiationpotential than do pluripotent stem cells. Another class of cells evenmore primitive (i.e., uncommitted to a particular differentiation fate)than pluripotent stem cells are the so-called “totipotent” stem cells(e.g., fertilized oocytes, cells of embryos at the two and four cellstages of development), which have the ability to differentiate into anytype of cell of the particular species. For example, a single totipotentstem cell could give rise to a complete animal, as well as to any of themyriad of cell types found in the particular species (e.g., humans). Inthis specification, pluripotent and totipotent cells, as well as cellswith the potential for differentiation into a complete organ or tissue,are referred as “primordial” stem cells.

“The morphology of positive control cell samples” can be determinedusing techniques that are well-known to those or ordinary skill in theart. For example, microtubule associated protein light chain 3(LC3) is aubiquitin-like protein that binds to autophagosomes (AVs). Mammaliancells can be transfected with GFP tagged LC3 to track and follow thefate of AVs in the cell and to measure autophagic flux. Also, GFP-LC3puncta that colocalize with mitochondria is a way to measure theinitiation of mitochondrial autophagy, the catabolic process by whichmitochondria are targeted for lysosomal degradation. See e.g. Chu, C.T., Plowey, E. D., Dagda, R. K., Hickey, R. W., Cherra I I I, S. J., andClark, R. S. Autophagy in Neurite Injury and Neurodegeneration: in vitroand in vivo models. Meth. Enzymol: 453:217-49, 2009; Dagda, R. K., Zhu,J., Kulich, S. M., and Chu, C. T. Mitochondrially localized ERK2regulates mitophagy and autophagic cell stress. Autophagy. 4 (6):770-82, 2008. PMID: 18594198; and Zhu J, Dagda R K, Chu C T. Monitoringmitophagy in neuronal cell cultures. Department of Pathology, Universityof Pittsburgh School of Medicine, Pittsburgh, Pa., USA. Methods MolBiol. 2011; 793:325-39, 2011.

As disclosed herein the invention enables the use of high-throughputformat, high-content imaging to examine the cell sample for anautophagy-associated effect on cytoplasmic puncta.

In one embodiment, determination of an autophagy-associated effect oncytoplasmic puncta involves detecting the amount of autophagy, or theamount of autophagosomes (AV) or AV activity, in a sample (e.g. a cell)both in the absence and presence of a candidate composition and anincrease or a decrease in the amount of autophagy as compared to controlindicates that the candidate composition is a modulator of autophagy ina cell extract, cell, tissue, organ, organism or individual.Fluorescence microscopy or a fluorescence imaging can be used todetermine the amount of and/or the location of the detectablecomposition or moiety in a sample cell. The screening, e.g.,high-throughput screening, method can comprise high-content imaging on amulti-well plate. The screening can be constructed and practiced on amulti-well plate. (Typically, wells are arranged in two-dimensionallinear arrays on the multi-well platform. However, the wells can beprovided in any type of array, such as geometric or non-geometricarrays. Commonly used numbers of wells include 24, 96, 384, 864, 1,536,3,456, and 9,600.) Transmission electron microscopy (TEM) can be used todetermine the amount of and/or the location of the detectablecomposition or moiety in the cell extract, cell, tissue, organ, organismor individual. This technique can be adapted to a plate-reader formatfor high-throughput screening of drugs that modulate autophagy, i.e.,high-throughput detection of autophagic (autophagosome) levels and/oractivity in cells or tissues. Compositions disclosed in U.S. PatentApplication Document No. 20120042398 (e.g., cadaverine derivatives) canlocalize into or detect autophagosomes (AV) or AV subpopulations, andthese compositions can comprise any detectable moiety or group, e.g.,cadaverine derivative(s), or fluorescent-, bioluminescent, radioactive-and/or paramagnetic-conjugated cadaverine reagents.

For generally applicable methods and materials that can be employed inthe use of high-throughput format, high-content imaging to examine acell sample for an autophagy-associated effect on cytoplasmic puncta,see: Eils et al., Concurrent detection of autolysosome formation andlysosomal degradation by flow cytometry in a high-content screen forinducers of autophagy. BMC Biology 2011, 9:38; Carragher, et al,Combining imaging and pathway profiling: an alternative approach tocancer drug discovery, Drug Discovery Today, Volume 17, Issues 5-6,March 2012, Pages 203-′.-214; and Methods in Enzymology Volume 506imaging and SpectrascopicAnalysis of Living Cells (Conn ed.) (2012).

In preferred embodiments, the methods of the invention are conducted ina high-throughput format.

Exemplary high-throughput assay systems include, but are not limited to,an Applied Biosystems plate-reader system (using a plate with any numberof wells, including, but not limited to, a 96-well plate, a-384 wellplate, a 768-well plate, a 1,536-well plate, a 3,456-well plate, a6,144-well plate, and a plate with 30,000 or more wells), the ABI 7900Micro Fluidic Card system (using a card with any number of wells,including, but not limited to, a 384-well card), other microfluidicsystems that exploit the use of TaqMan probes (including, but notlimited to, systems described in WO 04083443 A1, and published U.S.Patent Application Nos. 2003-0138829 A1 and 2003-0008308 A 1), othermicro card systems (including, but not limited to, W004067175 A1, andpublished U.S. Patent Application Nos. 2004-083443 A1, 2004-0110275 A1,and 2004-0121364 A1), the Invader® system (Third Wave Technologies), theOpenArray™ system (Biotrove), systems including integrated fluidiccircuits (Fluidigm), and other assay systems known in the art. Incertain embodiments, multiple different labels are used

in each multiplex amplification reaction in a high-throughput multiplexamplification assay system such that a large number of different targetnucleic acid sequences can be analyzed on a single plate or card. Incertain embodiments, a high-throughput multiplex amplification assaysystem is capable of analyzing most of the genes in a genome on a singleplate or card. In certain embodiments, a high-throughput multiplexamplification assay system is capable of analyzing all genes in anentire genome on a single plate or card. In certain embodiments, ahigh-throughput multiplex amplification assay system is capable ofanalyzing most of the nucleic acids in a transcriptome on a single plateor card. In certain embodiments, a high-throughput multiplexamplification assay system is capable of analyzing all of the nucleicacids in a transcriptome on a single plate or card.

The practice of the present invention may also employ conventionalbiology methods, software and systems. Computer software products of theinvention typically include computer readable medium havingcomputer-executable instructions for performing the logic steps of themethod of the invention. Suitable computer readable

medium include floppy disk, CD-ROM/DVD/DVD-ROM, hard-disk drive, flashmemory, ROM/RAM, magnetic tapes and etc. The computer executableinstructions may be written in a suitable computer language orcombination of several languages. Basic computational biology methodsare described in, for example Setubal and Meidanis et al., Introductionto Computational Biology Methods (PWS Publishing Company, Boston, 1997);Salzberg, Searles, Kasif, (Ed.), Computational Methods in MolecularBiology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler,Bioinformatics Basics: Application in Biological Science and Medicine(CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: APractical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc.,2.sup.nd ed., 2001). See U.S. Pat. No. 6,420,108.

The present invention may also make use of various computer programproducts and software for a variety of purposes, such as probe design,management of data, analysis, and instrument operation. See, U.S. Pat.Nos. 5,593,839, 5,795,716, 5,733,729, 5,974,164, 6,066,454, 6,090,555,6,185,561, 6,188,783, 6,223,127, 6,229,911 and 6,308,170.

Additionally, the present invention relates to embodiments that includemethods for providing information over networks such as the Internet.For example, the components of the system may be interconnected via anysuitable means including over a network, e.g. the ELISA plate reader tothe processor or computing device. The processor may take the form of aportable processing device that may be carried by an individual usere.g. lap top, and data can be transmitted to or received from anydevice, such as for example, server, laptop, desktop, PDA, cell phonecapable of receiving data, BLACKBERRY™, and the like. In someembodiments of the invention, the system and the processor may beintegrated into a single unit. In another example, a wireless device canbe used to receive information and forward it to another processor overa telecommunications network, for example, a text or multi-mediamessage.

The functions of the processor need not be carried out on a singleprocessing device. They may, instead be distributed among a plurality ofprocessors, which may be interconnected over a network. Further, theinformation can be encoded using encryption methods, e.g. SSL, prior totransmitting over a network or remote user. The information required fordecoding the captured encoded images taken from test objects may bestored in databases that are accessible to various users over the sameor a different network.

In some embodiments, the data is saved to a data storage device and canbe accessed through a web site. Authorized users can log onto the website, upload scanned images, and immediately receive results on theirbrowser. Results can also be stored in a database for future reviews.

In some embodiments, a web-based service may be implemented usingstandards for interface and data representation, such as SOAP and XML,to enable third parties to connect their information services andsoftware to the data. This approach would enable seamless datarequest/response flow among diverse platforms and software applications.

The term “compound” is used herein to refer to any specific chemicalcompound disclosed herein. Within its use in context, the term generallymay refer to a single compound, such as a polypeptide or other molecularentity used in the present invention.

In certain non-limiting embodiments, an increase or a decrease in asubject or test sample of the level of measured protein or geneexpression or autophagic change as compared to a comparable level ofmeasured protein or gene expression or autophagic change in a controlsubject or sample can be an increase or decrease in the magnitude ofapproximately ±5,000-10,000%, or approximately ±2,500-5,000%, orapproximately ±1,000-2,500%, or approximately ±500-1,000%, orapproximately ±250-500%, or approximately ±100-250%, or approximately±50-100%, or approximately ±25-50%, or approximately ±10-25%, orapproximately ±10-20%, or approximately ±10-15%, or approximately±5-10%, or approximately ±1-5%, or approximately ±0.5-1%, orapproximately ±0.1-0.5%, or approximately ±0.01-0.1%, or approximately±0.001-0.01%, or approximately ±0.0001-0.001%.

The values obtained from controls are reference values representing aknown health status and the values obtained from test samples orsubjects are reference values representing a known disease status. Theterm “control”, as used herein, can mean a sample of preferably the samesource (e.g. blood, serum, tissue etc.) which is obtained from at leastone healthy subject to be compared to the sample to be analyzed. Inorder to receive comparable results the control as well as the sampleshould be obtained, handled and treated in the same way. In certainexamples, the number of healthy individuals used to obtain a controlvalue may be at least one, preferably at least two, more preferably atleast five, most preferably at least ten, in particular at least twenty.However, the values may also be obtained from at least one hundred, onethousand or ten thousand individuals.

A level and/or an activity and/or expression of a translation product ofa gene and/or of a fragment, or derivative, or variant of saidtranslation product, and/or the level or activity of said translationproduct, and/or of a fragment, or derivative, or variant thereof, can bedetected using an immunoassay, an activity assay, and/or a bindingassay. These assays can measure the amount of binding between saidprotein molecule and an anti-protein antibody by the use of enzymatic,chromodynamic, radioactive, magnetic, or luminescent labels which areattached to either the anti-protein antibody or a secondary antibodywhich binds the anti-protein antibody. In addition, other high affinityligands may be used. Standard techniques for growing cells, separatingcells, and where relevant, cloning, DNA isolation, amplification andpurification, for enzymatic reactions involving DNA ligase, DNApolymerase, and restriction endonucleases as disclosed above can beemployed.

In exemplary embodiments of the invention which comprise detecting thepresence of antibodies that are reactive to caspase-I, antibodies arefound in a sample from a subject. The antibodies can be detected by animmunoassay wherein an antibody-protein complex is formed. Theantibodies are found in the sample of the subject, e.g. serum. Thesubject is a human and the implicated disease (e.g. tuberculosis) isidiopathic. Healthy individuals have minimal or undetectableanti-caspase-1 by conventional ELISA or Western blots. Individuals withidiopathic tuberculosis have significant amount of detectableanti-caspase-1 auto-antibodies, at least 10% more anti-caspase-1auto-antibodies detected over that from a healthy non-tuberculosisindividual or the level obtained for a population of healthynon-tuberculosis individuals by conventional ELISA or Western blots asdescribed herein. Moreover the levels of auto-antibodies correspond withthe clinical features of the disease condition. Patients in remissionafter effective treatment have minimal or undetectable anti-caspase-1auto-antibodies by conventional ELBA or Western blots. As an example, byundetectable amount of anti-caspase-I auto-antibodies, it means that novisible band is observed in a Western Blot analysis performed asdescribed in Example 1, wherein human serum is diluted 1:100 and used inblot assays described herein. In one embodiment, the amount ofanti-caspase-1 auto-antibodies in a healthy non-tuberculosis individualor the average amount in a population of healthy non-tuberculosisindividuals as determined by conventional ELISA or Western blot can beconsidered as the background, reference or the control level. Thecollected samples of serum from the healthy non-tuberculosis individualsare diluted 1:100 and used in Western blot assays. The intensity of thevisible band is quantified by densitometry. The densitometry intensitycan be calibrated with a range of known titer of anti-caspase-1antibodies reacting with a fixed amount of antigen caspase-1. Forexample, the range of known antibody titer can be O .mu.g/ml, 0.5.mu.g/ml, 1.0 .mu.g/ml, 1.5 .mu.g/ml, 2.0 .mu.g/ml, 2.5 .mu.g/ml, 3.0.mu.g/ml, 5 .mu.g/ml, 7.5 .mu.g/ml, 10 .mu.g/ml, and 15 .mu.g/ml and thefixed amount of caspase-1 can be 0.5 .mu.g on a blot. By comparing thedensitometry intensity of a human sample with the calibration curve, itis possible to estimate the titer of the anti-caspase-1 in the sample.For the data collected for a population of individuals, the averagevalue and one order of standard deviation is computed. Ideally, apopulation has about 25 healthy non-tuberculosis individuals, preferablymore. The statistics, the average value and one order of standarddeviation can be uploaded to the computer system and data storage media.Patients having at least 10% more than this average amount ofanti-caspase-1 auto-antibodies is likely to have tuberculosis,especially if the patient is also presents the clinical significantfeatures of the disease. Methodologies that are similar to thosedescribed above can be used to evaluate other targets and disordersdescribed herein.

In one embodiment, the auto-antibodies in the sample are reactiveagainst the caspase-1 that has been extracted from mammalian tissues orrecombinant mammalian caspase-1, e.g. the human caspase-1. The samplefrom the subject can be a blood sample. In other embodiments, the sampleis a serum or plasma sample. In one embodiment, the auto-antibodies aredetected by a serological immunoassay, such as an enzyme-linkedimmunosorbant assay or a nephelometric immunoassay.

The term “patient” or “subject” refers to an animal, such as a mammal,or a human, in need of treatment or therapy to which compounds accordingto the present invention are administered in order to treat a conditionor disease state associated with a tuberculosis infection orinflammation-associated metabolic disorder, for instance, a particularstage of an obesity-related disorder, using compounds according to thepresent invention.

An “inflammation-associated metabolic disorder” includes, but is notlimited to, lung diseases, hyperglycemic disorders including diabetesand disorders resulting from insulin resistance, such as Type I and TypeII diabetes, as well as severe insulin resistance, hyperinsulinemia, anddyslipidemia or a lipid-related metabolic disorder (e.g. hyperlipidemia(e.g., as expressed by obese subjects), elevated low-density lipoprotein(LDL), depressed high-density lipoprotein (HDL), and elevatedtriglycerides) and insulin-resistant diabetes, such as Mendenhall'sSyndrome, Werner Syndrome, leprechaunism, and lipoatrophic diabetes,renal disorders, such as acute and chronic renal insufficiency,end-stage chronic renal failure, glomerulonephritis, interstitialnephritis, pyelonephritis, glomerulosclerosis, e.g., Kimmelstiel-Wilsonin diabetic patients and kidney failure after kidney transplantation,obesity, GH-deficiency, GH resistance, Turner's syndrome, Laron'ssyndrome, short stature, increased fat mass-to-lean ratios,immunodeficiencies including decreased CD4+ T cell counts and decreasedimmune tolerance or chemotherapy-induced tissue damage, bone marrowtransplantation, diseases or insufficiencies of cardiac structure orfunction such as heart dysfunctions and congestive heart failure,neuronal, neurological, or neuromuscular disorders, e.g., diseases ofthe central nervous system including Alzheimer's disease, or Parkinson'sdisease or multiple sclerosis, and diseases of the peripheral nervoussystem and musculature including peripheral neuropathy, musculardystrophy, or myotonic dystrophy, and catabolic states, including thoseassociated with wasting caused by any condition, including, e.g., mentalhealth condition (e.g., anorexia nervosa), trauma or wounding orinfection such as with a bacterium or human virus such as HIV, wounds,skin disorders, gut structure and function that need restoration, and soforth.

An “inflammation-associated metabolic disorder” also includes a cancerand an “infectious disease” as defined herein, as well as disorders ofbone or cartilage growth in children, including short stature, and inchildren and adults disorders of cartilage and bone in children andadults, including arthritis and osteoporosis. An“inflammation-associated metabolic disorder” includes a combination oftwo or more of the above disorders (e.g., osteoporosis that is a sequelaof a catabolic state). Specific disorders of particular interesttargeted for treatment herein are diabetes and obesity, heartdysfunctions, kidney disorders, neurological disorders, bone disorders,whole body growth disorders, and immunological disorders.

In one embodiment, “inflammation-associated metabolic disorder”includes: central obesity, dyslipidemia including particularlyhypertriglyceridemia, low HDL cholesterol, small dense LDL particles andpostpranial lipemia; glucose intolerance such as impaired fastingglucose; insulin resistance and hypertension, and diabetes. The term“diabetes” is used to describe diabetes mellitus type I or type II. Thepresent invention relates to a method for improving renal function andsymptoms, conditions and disease states which occur secondary toimpaired renal function in patients or subjects with diabetes asotherwise described herein. It is noted that in diabetes mellitus type Iand II, renal function is impaired from collagen deposits, and not fromcysts in the other disease states treated by the present invention.

Mycobacterial infections often manifest as diseases such astuberculosis. Human infections caused by mycobacteria have beenwidespread since ancient times, and tuberculosis remains a leading causeof death today. Although the incidence of the disease declined, inparallel with advancing standards of living, since the mid-nineteenthcentury, mycobacterial diseases still constitute a leading cause ofmorbidity and mortality in countries with limited medical resources.Additionally, mycobacterial diseases can cause overwhelming,disseminated disease in immunocompromised patients. In spite of theefforts of numerous health organizations worldwide, the eradication ofmycobacterial diseases has never been achieved, nor is eradicationimminent. Nearly one third of the world's population is infected withmycobacterium tuberculosis complex, commonly referred to as tuberculosis(TB), with approximately 8 million new cases, and two to three milliondeaths attributable to TB yearly. Tuberculosis (TB) is the cause of thelargest number of human deaths attributable to a single etiologic agent(see Dye et al., J. Am. Med. Association, 282, 677-686, (1999); and 2000WHO/OMS Press Release).

Mycobacteria other than M tuberculosis are increasingly found inopportunistic infections that plague the AIDS patient. Organisms fromthe M avium-intracellulare complex (MAC), especially serotypes four andeight, account for 68% of the mycobacterial isolates from AIDS patients.Enormous numbers of MAC are found (up to 10¹⁰ acid-fast bacilli per gramof tissue), and consequently, the prognosis for the infected AIDSpatient is poor.

In many countries the only measure for TB control has been vaccinationwith M bovis bacille Calmette-Guerin (BCG). The overall vaccine efficacyof BCG against TB, however, is about 50% with extreme variations rangingfrom 0% to 80% between different field trials. The widespread emergenceof multiple drug-resistant M tuberculosis strains is also a concern.

M tuberculosis belongs to the group of intracellular bacteria thatreplicate within the phagosomal vacuoles of resting macrophages, thusprotection against TB depends on T cell-mediated immunity. Severalstudies in mice and humans, however, have shown that Mycobacteriastimulate antigen-specific, major histocompatibility complex (MHC) classII- or class I-restricted CD4 and CD8 T cells, respectively. Theimportant role of MHC class (-restricted CD8 T cells was convincinglydemonstrated by the failure of P2-microglobulin) deficient mice tocontrol experimental M tuberculosis infection.

As used herein, the term “tuberculosis” comprises disease states usuallyassociated with infections caused by mycobacteria species comprising Mtuberculosis complex. The term “tuberculosis” is also associated withmycobacterial infections caused by mycobacteria other than Mtuberculosis. Other mycobacterial species include Mavium-intracellulare, M kansarii, M fortuitum, M chelonae, M leprae, Mafricanum, and M microti, M avium paratuberculosis, M intracellulare, Mscrofulaceum, M xenopi, M marinum, M ulcerans.

An “infectious disease” includes but is limited to those caused bybacterial, mycological, parasitic, and viral agents. Examples of suchinfectious agents include the following: staphylococcus,streptococcaceae, neisseriaaceae, cocci, enterobacteriaceae,pseudomonadaceae, vibrionaceae, campylobacter, pasteurellaceae,bordetella, francisella, brucella, legionellaceae, bacteroidaceae,gram-negative bacilli, clostridium, corynebacterium, propionibacterium,gram-positive bacilli, anthrax, actinomyces, nocardia, mycobacterium,treponema, borrelia, leptospira mycoplasma, ureaplasma, rickettsia,chlamydiae, systemic mycoses, opportunistic mycoses, protozoa,nematodes, trematodes, cestodes, adenoviruses, herpesviruses,poxviruses, papovaviruses, hepatitis viruses, orthomyxoviruses,paramyxoviruses, coronaviruses, picomaviruses, reoviruscs, togaviruses,flaviviruses, bunyaviridae, rhabdoviruses, human immunodeficiency virusand retroviruses.

In certain embodiments, an “infectious disease” is selected from thegroup consisting of tuberculosis, leprosy, Crohn's Disease, acquiredimmunodeficiency syndrome, Lyme disease, cat-scratch disease, RockyMountain spotted fever and influenza or a viral infection selected fromHIV (I and/or II), hepatitis B virus (HBV) or hepatitis C virus (HCV).

“Autophagy-related immunomodulatory cytokines” include, but are notlimited to, IL-1a, IL-1, IL-18, IL-12p40 subunit, IL-4, IL 13, LMPI,EBNA2, IFN-γ, ATG16LI, IRGMI, LC3B-II, HMGB1 and TBK-I, among others.

“TBK-I agonists” include, but are not limited to, a vascular disruptingagent (VDA) such as lavone acetic acid and its derivatives, e.g., 5,6-dimethylxanthenone-4-acetic acid (DMXAA)).

“Caspase-I inhibitors” include, but are not limited to, minocycline,VX-765, IL-I8BP, Ac-YVAD.cmk, acetyl-Tyr-Val-Ala-Asp-chloromethylketone,N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone, zVAD-fmk,Z-Val-Ala-DL-Asp-fluoromethylketone, ML132 (CID-4462093; NCGC-00183434),(−)-berkeleyamide A (1), NCGCOO 185682, VRT-043198, the capsase-1inhibitors identified in Boxer, et al., ChemMedChem, 20 I 0 May 3;5(5):730-8, and N-Ac-Tyr-Val-Ala-Asp-chloromethyl ketone (Ac-YVAD-CMK).

“Autophagy-related immunomodulatory cytokine antagonists” include butare not limited to interleukin-I receptor antagonist (IL-IRA), humanrecombinant forms of IL-IRA, a vascular disrupting agent (VDA) such aslavone acetic acid and its derivatives, e.g., 5,6-dimethylxanthenone-4-acetic acid (DMXAA).

The term “biological sample” encompasses a variety of sample typesobtained from an organism and can be used in a diagnostic or monitoringassay. The term encompasses blood and/or plasma and other liquid samplesof biological origin, solid tissue samples, such as a biopsy specimen ortissue cultures or cells derived therefrom and the progeny thereof. Theterm encompasses samples that have been manipulated in any way aftertheir procurement, such as by treatment with reagents, solubilization,or enrichment for certain components. The term encompasses a clinicalsample, and also includes cells in cell culture, cell supernatants, celllysates, serum, plasma, biological fluids, and tissue samples.

The terms “body fluid” and “bodily fluid,” used interchangeably herein,refer to a biological sample of liquid from a mammal, e.g., from ahuman. Such fluids include aqueous fluids such as serum, plasma, lymphfluid, synovial fluid, follicular fluid, seminal fluid, amniotic fluid,milk, whole blood, urine, cerebrospinal fluid, saliva, sputum, tears,perspiration, mucus, tissue culture medium, tissue extracts, andcellular extracts. Particular bodily fluids that are interest in thecontext of the present invention include serum, plasma, and blood.

According to various embodiments, the compounds according to the presentinvention may be used for treatment or prevention purposes in the formof a pharmaceutical composition. This pharmaceutical composition maycomprise one or more of an active ingredient as described herein.

As indicated, the pharmaceutical composition may also comprise apharmaceutically acceptable excipient, additive or inert carrier. Thepharmaceutically acceptable excipient, additive or inert carrier may bein a form chosen from a solid, semi-solid, and liquid. Thepharmaceutically acceptable excipient or additive may be chosen from astarch, crystalline cellulose, sodium starch glycolate,polyvinylpyrolidone, polyvinylpolypyrolidone, sodium acetate, magnesiumstearate, sodium laurylsulfate, sucrose, gelatin, silicic acid,polyethylene glycol, water, alcohol, propylene glycol, vegetable oil,corn oil, peanut oil, olive oil, surfactants, lubricants, disintegratingagents, preservative agents, flavoring agents, pigments, and otherconventional additives. The pharmaceutical composition may be formulatedby admixing the active with a pharmaceutically acceptable excipient oradditive.

The pharmaceutical composition may be in a form chosen from sterileisotonic aqueous solutions, pills, drops, pastes, cream, spray(including aerosols), capsules, tablets, sugar coating tablets,granules, suppositories, liquid, lotion, suspension, emulsion, ointment,gel, and the like. Administration route may be chosen from subcutaneous,intravenous, intestinal, parenteral, oral, buccal, nasal, intramuscular,transcutaneous, transdermal, intranasal, intraperitoneal, and topical.The pharmaceutical compositons may be immediate release,sustained/controlled release, or a combination of immediate release andsustained/controlled release depending upon the compound(s) to bedelivered, the compound(s), if any, to be coadministered, as well as thedisease state and/or condition to be treated with the pharmaceuticalcomposition. A pharmaceutical composition may be formulated withdiffering compartments or layers in order to facilitate effectiveadministration of any variety consistent with good pharmaceuticalpractice.

The subject or patient may be chosen from, for example, a human, amammal such as domesticated animal, or other animal. The subject mayhave one or more of the disease states, conditions or symptomsassociated with autophagy as otherwise described herein.

The compounds according to the present invention may be administered inan effective amount to treat or reduce the likelihood of anautophagy-mediated disease and/or condition as well one or more symptomsassociated with the disease state or condition. One of ordinary skill inthe art would be readily able to determine an effective amount of activeingredient by taking into consideration several variables including, butnot limited to, the animal subject, age, sex, weight, site of thedisease state or condition in the patient, previous medical history,other medications, etc.

For example, the dose of an active ingredient which is useful in thetreatment of an autophagy mediated disease state, condition and/orsymptom for a human patient is that which is an effective amount and mayrange from as little as 100 μg or even less to at least about 500 mg ormore, which may be administered in a manner consistent with the deliveryof the drug and the disease state or condition to be treated. In thecase of oral administration, active is generally administered from oneto four times or more daily. Transdermal patches or other topicaladministration may administer drugs continuously, one or more times aday or less frequently than daily, depending upon the absorptivity ofthe active and delivery to the patient's skin. Of course, in certaininstances where parenteral administration represents a favorabletreatment option, intramuscular administration or slow IV drip may beused to administer active. The amount of active ingredient which isadministered to a human patient preferably ranges from about 0.05 mg/kgto about 10 mg/kg, about 0.1 mg/kg to about 7.5 mg/kg, about 0.25 mg/kgto about 6 mg/kg., about 1.25 to about 5.7 mg/kg.

The dose of a compound according to the present invention may beadministered at the first signs of the onset of an autophagy mediateddisease state, condition or symptom. For example, the dose may beadministered for the purpose of lung or heart function and/or treatingor reducing the likelihood of any one or more of the disease states orconditions which become manifest during an inflammation-associatedmetabolic disorder or tuberculosis or associated disease states orconditions, including pain, high blood pressure, renal failure, or lungfailure. The dose of active ingredient may be administered at the firstsign of relevant symptoms prior to diagnosis, but in anticipation of thedisease or disorder or in anticipation of decreased bodily function orany one or more of the other symptoms or secondary disease states orconditions associated with an autophagy mediated disorder to condition.

These and other aspects of the invention are described further in thefollowing illustrative examples.

Example 1 Autophagy is a Barrier Against Excessive Inflammation andActive Tuberculosis

Here we show that autophagy plays a dual role against tuberculosis:anti-bacterial and anti-inflammatory. Autophagy defect in Atg5fl/flLysM-Cre+ mice, infected with M tuberculosis, resulted in increasedbacillary burden and excessive pulmonary inflammation, neutrophilicinfiltration, and necrosis. This response was in part due to acell-autonomous pro-inflammatory phenotype. Autophagy-deficientmacrophages released excessive amounts of cytokines delivered byconventional and unconventional secretory pathways. The mechanism forexcessive secretion was determined for the cytosolic alarmin IL-1α:caspase 1, required for unconventional secretion of IL-1α, wasdownregulated by autophagy. IL-1α induced IL-17 in CD4 T cells inkeeping with neutrophilic inflammatory state. Thus, autophagy protectsagainst M tuberculosis and prevents uncontrolled inflammation leading totissue necrosis characteristic of active tuberculosis disease.

INTRODUCTION

Despite M tuberculosis being one of the first recognized microbessubject to elimination by immunological autophagy in ex vivo systems inmurine and human macrophages (Alonso et al., 2007; Gutierrez et al.,2004; Harris et al., 2007; Kim et al., 2011; Xu et al., 2007; Yuk etal., 2009a), the in vivo role of autophagy in control of M tuberculosishas not been reported, although genetic evidence nevertheless indicatesthat at least one of the autophagic factors (Singh et al., 2006; Singhet al., 2010) involved in Crohn's disease (Craddock et al., 2010;Mccarroll et al., 2008) may predispose human populations to tuberculosis(Intemann et al., 2009). Given the compelling reasons to test whetherautophagy matters for control of M tuberculosis in vivo, here we used amouse model of tuberculosis and employed transgenic mice deficient inAtg5 in macrophages, the cell type parasitized by M tuberculosis (Vergneet al., 2004). We demonstrate that autophagy controls tuberculosisinfection in vivo and uncover a potentially key role of autophagy incontaining the inflammatory reactions of the host. When autophagy isdeficient in the macrophages of infected mice, not only does this permitbacterial growth but also leads to an excessive proinflammatoryresponse, with partial roots in sterile inflammation, leading to lungtissue destruction, necrosis and active tuberculosis. Thus, in additionto the demonstration that autophagy controls M tuberculosis in vivo, ourdata indicate that autophagy represents a barrier against tissuedestruction, the hallmark of active disease and the necessary infectionstage for the propagation of tuberculosis in human populations.

Results

Autophagy Protects Micefrom Excessive Lungpathology Following AerogenicInfection with M tuberculosis

The in vivo role of autophagy was investigated by selective geneticdeletion of Atg5 in myeloid cells, with macrophages being of principalinterest as the cells both successfully parasitized by intracellular Mtuberculosis (Vergne et al., 2004) and targeted by protective immuneresponses. We used the previously reported conditional gene knockoutmouse model Atg5fl/fl LysM-Cre+ with Atg5 deletion in myeloid lineage(Zhao et al., 2008). The Atg5+ mice (Atg5fl/fl LysM-Cre−) and theirAtg5fl/fl LysM-Cre+ littermates, previously characterized for lack ofAtg5 and autophagy in macrophages (Dupont et al., 2011), were subjectedto aerogenic infection with virulent M tuberculosis H37Rv. A majorweight loss was observed in the infected Atg5-deficient mice compared toAtg5-proficient mice (FIG. 1A) when mice were infected with 103 Mtuberculosis cfu (lung deposition infectious dose termed e3;Supplementary Table 1). This was accompanied by lung pathologyremarkable for gross tubercle lesions in contrast to smaller infectedfoci in the lungs of Atg5+ animals (FIG. 1B). Microscopic examination ofAtg5fl/fl LysM-Cre+ lung tissue revealed massive lesions showing poorcellular organization and extensive necrotic centers, with veterinarypathologist findings described in Supplementary Materials (Figure IC).Acid fast bacilli, with prominence of extracellular bacteria, werenotable in Atg5fl/fl LysM-Cre+ compared to Atg5fl/fl LysM-Cre− lungsections (FIG. 1C). Unlike the infected Atg5fl/fl LysM-Cre+ lungs, thelungs from the infected Atg5fl/fl LysM-Cre− mice had fewer intracellularbacilli with little to no extracellular bacilli present in the lungsections (FIG. 1C).

In keeping with the well-known general resistance of mice totuberculosis, neither group of mice succumbed to the infection in shortterm (36 days) experiments (Supplementary Table 1). When a higherinfection dose (e4; lung disposition of 104 cfu Supplementary Table 1)was employed, this resulted in animal mortality with accelerated deaths(along with weight loss) among Atg5fl/fl LysM-Cre+ mice relative totheir Atg5fl/fl LysM-Cre− littermates, starting 20 days post infection(FIG. 1D,E). With the most commonly used low infectious dose (e2; lungdisposition of 102 cfu), the Atg5fl/fl LysM-Cre+ mice displayedincreased lung gross pathology and organ size/weight of both lungs andspleens (Suppl. FIG. 1A-C), poorer cellular organization and morenecrosis (Suppl. FIG. 1D), increased infiltration of innate immune cellsinto the lungs (Suppl. FIG. 1E-G), and more acid fast bacilli in lungsections (Suppl. FIG. 1H). The lungs of e2 infected animals showed aten-fold increase in cfu recovered from Atg5fl/fl LysM-Cre+ micerelative to their Atg5fl/fl LysM-Crelittermates (Suppl. FIG. 1H).

These data collectively show that Atg5^(fl/fl) LysM-Cre+ mice are moresusceptible to M tuberculosis infection and display increasedinflammation and lung pathology over a range of infectious doses

Atg5 Deficiency Increases Basal Immune Activation State in theUninfected Lung

Given the large differences in lung gross and histopathology and arelatively small detectable difference in bacterial loads betweeninfected Atg5fl/fl LysM-Cre+ and Atg5^(fl/fl) LysM-Cre− mice (Suppl.FIG. 1H), we considered the possibility that, apart from the directeffects in eliminating mycobacteria from macrophages as previouslyestablished in vitro (Alonso et al., 2007; Gutierrez et al., 2004;Harris et al., 2007; Kim et al., 2011; Xu et al., 2007; Yuk et al.,2009a), autophagy in myeloid cells may be necessary for innate immunecellular homeostasis or function to prevent an excessive response toinfection. We tested whether indications of such alterations may bedetectable in animals not infected with M tuberculosis, since infectionwould complicate interpretations. Similar numbers of cells expressingmacrophage markers, F4180+CD11b+(Lineage-negative: CD3− CD19−), weredetected in the lungs and bone marrow of uninfected Atg5fl/fl LysMCre+and Cre− mice (FIG. 2A,B). However, lung macrophages obtained fromuninfected Atg5^(fl/fl) LysM-Cre+ mice displayed an activated phenotype(FIG. 2C), in keeping with their general in situ morphology (Suppl. FIG.2A; inset). Specifically, Atg5^(fl/fl) LysM-Cre+ cells had increasedexpression of MHC class II, DEC205, and CD86. An increase in the numbersof CD11b+ F4/80− cells was observed in uninfected Atg5^(fl/fl) LysM-Cre+mice (FIG. 2A). Further examination revealed that these cells wereLy6G+(1a8 clone) polymorphonuclear granulocytes (PMN; neutrophils) (FIG.2D). This increase in PMN total number was only observed in the lungs,as bone marrow PMN numbers were comparable for both groups of mice (FIG.2E). These data indicate that autophagy in myeloid cells of peripheralorgans such as lungs, where continual immune surveillance is necessary,maintains a homeostatic balance of immune cells and their activationsstates under normal physiological conditions.

Atg5-Deficiency in Myeloid Lineage Results in Excessive InflammatoryCytokine Response to Infection

We examined cytokine profiles (using Luminex technology) during thecourse of e² infection in the lungs of Atg5^(fl/fl) LysM-Cre+ andAtg5fl/fl LysM-Cre− littermates. Within the broad panel of cytokines andchemokines tested, the e²-infected Atg5fl/fl LysM-Cre+ lungs displayed asignificant increase in the cytokines IL-1α and IL-12 and a chemokine,CXCL1, at different time points of infection (FIG. 3A-C). Additionalincreases were observed for IL-1β (albeit the absolute levels were low)and GM-CSF with no differences in IL-6 and the chemokine (Suppl. FIG.3A-D). We did not see a major difference in IFN-γ and TNFα the wellestablished anti-tuberculosis cytokines (Flynn and Chan, 2001), or IL-4,an intracellular pathogen-permissive cytokine known to inhibit autophagyex vivo (Harris et al., 2007) (Suppl. FIG. 3E-G). A difference in IL-17levels was detected (Suppl. FIG. 3H). To test whether cytokine increasesin the lungs of infected Atg5^(fl/fl) LysM-Cre+ animals hadcell-autonomous and infection-independent roots based on defectiveautophagy in relevant cell types, we compared bone marrow macrophages(BMM) from uninfected Atg5^(fl/fl) LysM-Cre+ mice and Atg5fl/flLysM-Cre− littermate controls. Uninfected BMM were stimulated with IFN-γand the TNF-α mimetic LPS, with IFN-γ and TNF-α being two key cytokinesdriving the responses to M. tuberculosis infection. Remarkably,Atg5^(fl/fl) LysM-Cre+ BMM recapitulated the in vivo pattern of elevatedcytokine secretion and displayed increased release of IL-1α, IL-12p70and CXCL1 relative to Atg5^(fl/fl) LysM-Cre− BMM (FIG. 3D-F).Differential IL-1α release was not due to changes in cell death ormembrane permeability since in vitro activated BMM from Atg5^(fl/fl)LysM-Cre+ and Atg5^(fl/fl) LysM-Cre− mice showed no difference instaining with 7-AAD (Suppl. FIG. 3I). Furthermore, Atg5^(fl/fl)LysM-Cre+ and Atg5 LysM-Cre− showed differential release of only asubset of cytokines, including IL-12p70 and CXCL1 that, unlike IL-1α,utilize the biosynthetic pathway and traffic through the lumen ofER-Golgi-post-Golgi organelles for active secretion from the cells.Intracellular IL-12p35 was also shown via flow cytometry to be increasedin stimulated BMM lacking Atg5 relative to Atg5-proficient BMM (Suppl.FIG. 3J,K), A subset of the above in vitro findings showing elevatedcytokine secretion were corroborated in vivo using lung homogenates ofuninfected Atg5fl/fl LysM-Cre+ and Cre− mice (FIG. 3D-F). Atg5^(fl/fl)LysM-Cre+ lung samples had significantly increased amounts of IL-1α andCXCL1 compared to Atg5^(fl/fl) LysM-Cre− lungs (FIG. 3G,H). IL-12p70 wasbelow the limit of detection in uninfected lung homogenates and couldnot be assessed in this way. Conversely, the chemokine, CXCL2, which wasexpressed at similar levels in the presence or absence of an intactautophagy pathway in BMM examined in vitro, was increased in Atg5fl/flLysM-Cre+ lung homogenate (Suppl. FIG. 3L,M). These results revealedadditional complexities in vivo, but nevertheless validated both in vivoand in vitro the elevated IL-1α and CXCL1 phenotype in Atg5fl/flLysM-Cre+ lungs and macrophages.

Autophagy is Essential for the Regulation of IL-1α Secretion.

We next focused on the cell-autonomous IL-1 hypersecretion phenotype inAtg5^(fl/fl) LysM-Cre+ macrophages. IL-1α is a cytosolic protein,produced as a proform processed during activation by proteases such ascalpain or alternative proteolytic enzymes (Afonina et al., 2011) andactively exported out of the cell (Yazdi et al., 2010) or passivelyreleased upon cell death (Chen et al., 2007). We first confirmed thatautophagy was a negative regulator of IL-1α release by pharmacologicallymanipulating autophagy in autophagy-competent macrophages. Whenautophagy was induced with rapamycin in Atg5fl/fl LysM-Cre− BMM thisreduced the amount of IL-1α, being secreted (FIG. 4A). Conversely, whenAtg5fl/fl LysM-Cre− BMM were treated with 3-methyladenine, an inhibitorof autophagosome formation, the levels of IL-1α were significantlyincreased (FIG. 4A) mimicking a condition observed upon geneticdisabling of autophagy. A similar trend was observed when bafilomycinA1, an inhibitor of autophagic flux was added during stimulation (FIG.4B). The results of pharmacological modulation of autophagy in normalBMM validated the conclusions derived with Atg5^(fl/fl) LysM-Cre+ BMMthat autophagy negatively regulates IL-1α activation and secretion.

Cell-Autonomous Hypersecretion Phenotype in Autophagy-DeficientMacrophages is not Secondary to Autophagic Effects an p62 or Calpain

To delineate the mechanism of how autophagy controls IL-1α activationand secretion we considered several levels and factors that couldpotentially mediate the effects of the absence of autophagy. Theautophagic adaptor protein p62, which is consumed during autophagy (Jainet al., 2010) and is the founding member of the SLR family of PRRfunctions in innate immunity signaling (Deretic, 2011), accumulates inthe absence of autophagy pathway and has been shown to perturb NF-κBresponses (Mathew et al., 2009; Moscat and Diaz-Meco, 2009). As IL-1αexpression is induced by NF-κB (Xia et al., 1999), p62 accumulationcould be the cause of elevated IL-1α expression. However, knocking downp62 via siRNA in Atg5^(fl/fl) LysM-Cre+ BMM (Suppl. FIG. 4A) did notabrogate the elevated IL-1α secretion by these cells (Suppl. FIG. 4B). Aconverse experiment was also carried out. Atg5 was knocked down in BMMfrom p62−/− knockout mice and this still caused more (albeit lesspronounced likely due to residual Atg5 levels) IL-1α secretion than inthe scrambled siRNA control (Suppl. FIG. 4C). Finally, no increase inIL-1α mRNA levels were detected in Atg5^(fl/fl) LysM-Cre+ BMM relativeto Atg5fl/fl LysM-Cre− BMM (Suppl. FIG. 4D), thus establishing thatAtg5-deficient cells are neither transcriptionally pre-activated forIL-1α expression nor that p62 contributes to the IL-1α phenotype. Sincecalpain activates IL-1α, we used ALLN, a calpain inhibitor, to testwhether calpain was involved in the IL-1α hyper-secretion phenotype ofAtg5fl/fl LysM-Cre+ cells. ALLN treatment of Atg5fl/fl LysM-Cre+completely abrogated the excess IL-1α production normalizing itssecretion to the levels seen with Atg5fl/fl LysM-Crecells (FIG. 4C).Hence, we considered the possibility that calpain was involved inmediating differences between Atg5fl/fl LysM-Cre+ and Atg5fl/flLysM-Cre+ cells, and that it could be a substrate for autophagicremoval. However, calpain and LC3 did not colocalize in the cytoplasm,as indicated by a negative Pearson's colocalization coefficient inbafilomycin A1-treated cells that would have preserved calpain inautophagic organelles due to inhibition of autophagic flux anddegradation (Suppl. FIG. 5A,B). Most importantly, the intracellularlevels of calpain were similar in Atg5fl/fl LysM-Cre+ and Atg5fl/flLysM-Cre BMM (Suppl. FIG. 5C, D).

Factor X is Responsible for Hypersecretion of IL-1α in the Absence ofAutophagy

Next we studied whether IL-1α is a direct target for removal inautophagic organelles. When autophagy-competent BMM (Atg5^(fl/fl)LysM-Cre−) were examined by fluorescent confocal microscopy, cells fellinto two categories—those that were positive for IL-1α punctuatestaining and those that were positive for LC3 puncta (FIG. 4D) with veryfew cells that were positive for both IL-1α established by a χ2 test(χ2<0.02; Suppl. Figure [[S]]4E). This observation was initially takenas an indication that IL-1α may be targeted by autophagy fordegradation, so we proceeded by examining whether bafilomycin A1treatment could spare IL-1α. Indeed, bafilomycin A1 treatment increasedthe number of cells positive for both EL-1α and LC3 (FIGS. 4E and F)with nonrandom distribution (Suppl. Figure S4E; χ2<0.95). However, LC3and IL-1α did not colocalize (FIGS. 4E and 5A,B), suggesting that it isnot IL-1α that is a direct Substrate for autophagic elimination. Thisled us to postulate the existence of a putative factor, dubbed factor X,regulating IL-1α in some way, e.g. amounts or secretion, was a substratefor autophagy.

Factor X is Caspase 1

In considering the candidates for factor X, we were aided by the recentreports that alarmins, including IL-1α, that are not conventionalsubstrates for inflammasome can nevertheless be affected by a platformsimilar to that which controls the conventional caspase 1 substrateIL-1β (Fettelschoss et al., 2011; Keller et al., 2008; Yazdi et al.,2010). In contrast to the negative Pearson's colocalization coefficientfor IL-1α and LC3, caspase 1 and LC3 showed positive colocalization(FIG. 5A,B). Next, BMM were tested for caspase 1 levels and activation.Atg5fl/fl LysM-Cre+ BMM showed increased levels of activated caspase 1(p20) in comparison to Atg5^(fl/fl) LysM-Cre− BMM, whereas pro-caspase 1levels did not differ (FIG. 5C and Suppl. FIG. 5E). Bafilomycin A1treatment resulted in abnormally higher levels of caspase 1 p20 inAtg5fl/fl LysM-Cre− BMM mimicking the state of Atg5^(fl/fl) LysM-Cre+cells (FIG. 5C and Suppl. FIG. 5E). Furthermore, caspase 1 activitymeasured by FLICA assay demonstrated increased enzymatically activeCaspase 1 in Atg5fl/fl LysM-Cre+ BMM compared to Atg5fl/fl LysM-Cre− BMM(Suppl. FIG. 5F). Finally, IL-1α secretion was further increased fromautophagy-defective BMM in response to silica, which is a conventionalinflammasome agonist (FIG. 5D). We conclude that factor X is caspase 1and that it is normally targeted by autophagy for downregulation.Caspase 1 is increased in amounts and activity in autophagy-defectivemacrophages, and is a contributor to the cell-autonomous phenotype ofelevated IL-1α secretion observed in our experiments with Atg5^(fl/fl)LysM-Cre+ macrophages.

Functional Autophagic Machinery in Macrophages Dictates CD4 T CellPolarization and Regulates IL-17 Response

The activated macrophages, PMN infiltrates, cytokines and chemokinespresent in the lung of uninfected Atg5fl/fl LysM-Cre+ mice suggestedfeatures of a Th1 7 response (Chung et al., 2009; Korn et al., 2009). Weconsidered this further. First, we determined the proportion of CD8 andCD4 T cells displaying an activated/memory phenotype. CD44 and CD25expression was examined on both CD8 and CD4 T cells. The proportion of Tcells displaying an activated/memory phenotype (CD44high) wassignificantly increased for both CD8 and CD4 populations in Atg5fl/flLysM-Cre+ mice (FIG. 6A, Suppl. FIG. 6A). A portion of the CD44high CD4T cells were also positive for CD25 suggesting that these cells wererecently activated (FIG. 6A). To determine if these T cells werepolarized to a certain subset of helper T cells we stimulated total lungleukocytes with PMA/ionomycin (plus protein transport inhibitors) andthen assessed intracellular levels of IL-17A and IFN-γ expressed by CD4T cells. CD4 T cells from Atg5fl/fl LysM-Cre+ lungs but not those fromAtg5fl/fl LysM-Cre− lungs produced IL-17A (FIG. 6B,C). There was nomarked difference between the same cells from two sources in theirability to mount IFN-γ response (FIG. 6B.C). These findings indicate apropensity of CD4 T cells from Atg5fl/fl LysM-Cre+CD4 T cells to produceIL-17A upon stimulation.

Defective Autophagy in Myeloid Lineage of Atg5fl/fl LysM-Cre+ MicePromotes IL-17 Response to Defined Jv1 Tuberculosis Antigens by T Cells

The cells from the lungs of kl tuberculosis infected Atg5fl/fl LysM-Cre+and Cremice revealed little difference in key Th 1 and Th2 cytokines asdescribed above. However, a trend was observed for more I L-17 ininfected Atg5fl/fl LysM-Cre+ mice (Figure S3E-H). We followed up on thislead using a cocktail of 5 well defined Jv1 tuberculosis proteinantigens (DnaK, GroEL, Rv009, Rv0569, Rv0685), collectively referred toas synthetic PPD (Yang et al., 201 1) in reference to the purifiedprotein derivative (PPD) used clinically as tuberculin skin test forevidence of recent tuberculosis infection or BCG vaccination. Th issynthetic reagent contains the dominant antigens present in theconventional PPD, includes additional key immunogenic proteins.Synthetic PPD reproduces the anatomical and molecular properties of thetuberculin skin test and eliminates false positive inflammatoryreactions (seen in uninfected hosts) caused by the contaminatinglipoglycans and carbohydrates resident in conventional PPD, thusenabling monitoring of specific responses to infection with the Jv1tuberculosis complex organisms in a model system (Yang et al., 201 1).Atg5fl/fl LysM-Cre+ and Cre− mice were infected with live M. bovis BCGand then evaluated for their ability to mount a delayed typehypersensitivity response (0TH) to synthetic PPD (Yang et al., 20 t 1).Three weeks postinfection, mice were injected with the synthetic PPD orPBS in the hind footpad and swelling was measured at 0, 2, 24 and 48 hpostinoculation (FIG. 6C). No measurable difference was observed at 24and 48 h time point between the autophagy competent and mutant mice.However, when splenocytes were re-stimulated ex vivo with the syntheticPPD, IL-17A was detected at a significantly higher levels with Atg5fl/flLysM-Cre+ splenocyte supernatant whereas no differences were observedfor typical Th 1 and Th2 cytokine signatures (FIG. 6D,E; Suppl. FigureS6B,C) indicating polarization to IL-17 producing phenotype in Atg5fl/flLysM-Cre+ mice. Finally, we tested whether IL-1 a, observed in excess inAtg5fl/fl LysM-Cre+ lungs or with Atg5fl/fl LysM-Cre+ BMM could actsimilarly to IL-1p in promoting Th 17 polarization (Chung et al., 2009).Naïve CD4 T cells were treated in the presence of TGF-P, IL-6 and IL-1aor IL-1 B and then stimulated in the presence of protein transportinhibitors. The intracellular levels of IL-17A were elevated whether. IL-1a or IL-1 P were used to promote Th 17 differentiation (FIG. 6F).

These data sets indicate that a dysregulation in the autophagic pathwayin macrophages can result in an in situ generation of IL-J 7-producing Tcells via the excess production of IL-1a.

Discussion

This work demonstrates the in vivo role for autophagy in protectionagainst tuberculosis. Along with the previous in vitro studies (Alonsoet al., 2007; Gutierrez et al., 2004; Harris et al., 2007; Hartman andKornfeld, 2011; Kim et al, 2011; Xu et al., 2007; Yuk et al., 2009a)this establishes that autophagy is an antimycobacterial effectormechanism. Autophagy also protects against excessive tissue necrosis andlung pathology, the hallmarks of active tuberculosis. This effect is nota trivial consequence of increased bacillary loads but reflects acell-autonomous action of autophagy as shown in vitro with macrophagesfrom uninfected animals. In addition to the expected immune activationcommensurate with bacterial loads, autophagy-defective macrophages havean intrinsic propensity to release excessive amounts of inflammatorymediators IL-1a and CXCL1, shown in vitro and mirrored in vivo inuninfected lungs. A model emerges whereby these mediators pivotinflammation with features of Th 17 response, neutrophilic infiltration,tissue necrosis and organ damage, the main features of activetuberculosis and contagious state of the host.

The mechanisms of cell-autonomous elimination of M tuberculosis byautophagy have been extensively studied in vitro and include directmicrobial digestion in autophagolysosomes (Gutierrez et al., 2004),delivery of neoantimicrobial peptides generated in autolysosomes tocompartments harboring intracellular mycobacteria (Alonso et al., 2007;Kim et al., 2011; Ponpuak et al., 2010) and an interplay of autophagywith conventional antimicrobial peptides (Yuk et al., 2009b). Ourprevious work (Ponpuak et al., 2010) has highlighted the role of the SLRp62 in these processes, along with the examples of other SLRs engagingan array of intracellular bacteria (Deretic, 2011; Dupont et al., 2009;Thurston et al., 2009; Wild et al., 2011; Yoshikawa et al., 2009) andviruses (Orvedahl et al., 2010). The work presented in the accompanyingstudy by J. Cox and colleagues extends this further and places the roleof SLRs in the context of the ESXdependent interactions between Mtuberculosis and the host cell cytosol. In contrast to a preponderanceof studies in vitro, autophagic control of microbes remains to be fullyunderstood in vivo (Orvedahl et al., 2010; Zhao et al., 2008). Alteredintestinal tissue and Paneth cell function has been noted in response tomicrobial flora and viral co-infection in an Atg16L1 hypomorph mousemodel of Crohn's disease, a chronic inflammatory condition [Cadwell,2010 #13743]. In the animal model of protection against lethal Sindbisvirus infection, the dominant contribution of autophagy was inpreventing tissue damage independently of viral loads (Orvedahl et al.,2010). This dovetails with the aspect of our study that shows autophagicprotection against excessive inflammation and necrosis in the murinemodel of tuberculosis.

The finding that a loss of autophagy in macrophages results in increasedrelease of IL-1α and CXCL 1 and fosters an environment where T cellsproduce IL-17A production links for the first time autophagy withelements of the Th 17 response. The increased presence of neutrophils inthe lungs of Atg⁵fl/fl LysM-Cre+ mice infected with M tuberculosis wasconsistent with lung tissue damage and progressive disease. The role ofneutrophils in tuberculosis has been both highlighted in recent patientcohort studies (Berry et al., 2010) and may be associated with theparadoxical Koch effect (Koch, 1891), whereby administration of Mtuberculosis antigens to pre-infected subjects increases granulocyteinflux and necrosis in the preexisting stabilized lesions in the lung(Moreira et al., 2002; Taylor et al., 2003; Turner et al., 2000).Neutrophils contribute to tuberculosis pathogenesis (Eruslanov et al.,2005), support lymphatic mycobacterial dissemination (Abadie et al.,2005), and promote person-to-person transmission via cavitary disease orother routes of bacillary delivery into patients' sputa (Eum et al.,2010), outweighing potential antibacterial actions of neutrophils. Ourdata indicate that autophagy, when functional, curbs neutrophilicresponse.

A specific dysregulated cytokine response in Atg⁵fl/fl LysM-Cre+ micefor which a cell-autonomous molecular mechanism has been determined inthis work is the excessive release of IL-1α. IL-1 signaling has beenimplicated in defense against M tuberculosis but presents a host ofnon-trivial relationships. IL-1p and its receptor IL-1RI have beenassociated with the powerful antimycobacterial role of MyD88 (Fremond etal., 2007; Mayer-Barber et al., 2010), an adaptor downstream of IL-1RIand other pattern recognition receptors. Mycobacterial products caninduce inflammasome, caspase 1, and IL-1p production (Mishra et al.,2010) and virulent M tuberculosis actively suppresses inflammasomeactivation and IL-I P production in vivo (Master et al., 2008). Theeffector mechanisms downstream of IL-1 signaling include autophagy as amycobactericidal mechanism activated by IL-I P via MyD88 (Pilli et al.,submitted). Nevertheless, not all aspects of IL-1 signaling areprotective. IL-I P suppresses IFN-y production and Th 1 polarization byinducing COX-2 and promotes Th1 7 responses causing neutrophil-dominatedinflammation (van de Veerdonk et al., 2011). Whereas beneficial incontrol of extracellular bacteria, these features may not be desirableagainst M tuberculosis as discussed above and instead may contribute toimmunopathology. This is in keeping with the findings that excess IL-17Aand potentially other Th1 7 cytokines and neutrophil chemokines candeleteriously enhance lung pathology during M tuberculosis infection(Cruz et al., 2010). As observed in present study, IL-1a can affectaspects of Th1 7 polarization as effectively as IL-1 p. It has beenreported that the abundant presence of IL-1α in IL-1P-deficient mice(Mayer-Barber et al., 2010) cannot compensate for the lack of IL-1 P,arguing that IL-1a may not have the anti-mycobacterial potency orbioavailability as IL-1 P, which suggest that IL-1a may be primarilypathogenic. Nevertheless, the results of two recent studies (Guler etal., 2011; Mayer-Barber et al., 2011) indicate that IL-1a is required tocontrol tuberculosis at a yet to be defined stage during immune responseor tissue remodeling. Thus, any therapeutic strategies aiming atneutralizing IL-1a specifically to curb tissue destruction andneutrophilic contribution to contagious state in active disease willhave to await further studies.

IL-1a is produced as a cytosolic proc.form that can be processed bycalpain or other proteases (Afonina et al., 2011) and actively exportedout of the cell as shown here and elsewhere (Yazdi et al., 2010) or bepassively released upon cell death (Chen et al., 2007). The IL-1asecretion, normally suppressed by basal autophagy as detected here wasan active process of unconventional secretion from macrophages, inkeeping with macrophages being one of the major sources of secretedIL-1a in certain forms of inflammation (Kono et al., 2010). The cellularmechanism of excessive IL-1a release was linked to increasedintracellular active caspase-1 in Atg⁵fl/fl LysM-Cre+ macrophages.Although surprising, this is in keeping with the growing evidence(Fettelschoss et al., 2011; Keller et al., 2008; Lamkanfi, 2011;Lamkanfi et al., 2010; Willingham et al., 2009; Yazdi et al., 2010) thatvarious inflammasome components contribute to extracellular release ofsubstrates other than the canonical caspase-1-processed targets such asIL-1p (Dinarello, 2009). Like IL-1P, the alarmins HGMB1 (Keller et al.,2008; Lamkanfi, 2011; Lamkanfi et al., 2010; Willingham et al., 2009)and IL-1a (Fettelschoss et al., 2011; Keller et al., 2008; Yazdi et al.,2010) are subject to unconventional secretion and are affected byinflammasome components although they are not proteolytically processedby caspase-1 (Johansen et al., 2011; Keller et al., 2008; Lamkanfi,2011; Lamkanfi et al., 2010; Willingham et al., 2009; Yazdi et al.,2010). The mechanism for hypersecretion of IL-12 and CXCL1 by Atg5fl/flLysM-Cre+ macrophages was not determined. We favor the possibility thatthese cytokines, which utilize the conventional secretory pathway, areinfluenced by the recently described specific intersections between theorganelles of the biosynthetic secretory pathway and autophagy as shownin the case of IL-6 (Narita et al., 2011).

Tuberculosis has been and remains one of the main global public healthhazards further augmented by the HIV co-pandemic (Nunn et al., 2005).The classical presentation of disease is often masked by the untreatedHIV co-infection (Nunn et al., 2005), but in principle the majority ofhumans have a well developed capacity to contain the infection so thatthe majority of the world's population infected with the tuberclebacillus is asymptomatic and only approximately 10% of individualsdevelop active disease. This tip of the iceberg is nevertheless key tocontinuing the tuberculosis contagion in human populations, since activedisease is necessary for the transmission of tuberculosis. We proposethat autophagy plays a dual role: it both protects against the microbeand guards against host-inflicted tissue destruction and active disease.In this model autophagy curbs tuberculosis transmission by helpingmaintain the majority of the infected population asymptomatic.Strategies aimed at pharmacological manipulation of autophagy maydiminish tuberculosis spread, which may prove vital in containing thespread of the increasingly drug-resistant tuberculosis strains.

Experimental Procedures

Mice, Infection, Cells. Flow Cytometry and Immunodetection Methods

The transgenic Atg⁵fl/fl LysM-Cre+(myeloid specific Atg5 deletion) andAtg⁵fl/fl LysM-Cre− mice have been previously characterized [Zhao, 2008#6094] and the autophagy defect in BMM extensively documented [Dupont,2011 #14374]. LC3-GFP knock-in transgenic mice [Mizushima, 2004 #17] andp62−/− knockout mice [Komatsu, 2007 #5273] have been previouslydescribed. Mice were maintained under specific pathogen-free conditions.F1 progeny from Atg⁵fl/fl LysM-Cre×Atg⁵fl/fl crosses were genotyped forpresence (LysM-Cre+) or absence (LysMCre) of the LysM-Cre allele byTransnetyx Inc. (Cordova, Tenn.). Infection studies

were carried out using murine respiratory infection model [Flynn, 2008#5138] and virulent M tuberculosis H37Rv with modifications [Talaat,2004 #14428][Zahrt, 2001 #1633] described in supplementary materials.All cells were pretreated with Stain FcX (anti-CD 16/32) (Biolegend)before being stained for: CD14 (Sa14-2), F4/80 (BM8), IFN-y (XMG 1.2),IL-17A (TC11-18H10.1), CD11b (M1/70), DEC205 (NLDL-145), CDS (53-6.7),CD86 (GL-1), Ly6G (1A8), CD25 (PC61), MHC II (M5/114.15.2) (Biolegend).CD19 (eBioID3), TCR (H57-597), CD3e (145-2C11), CD44 (IM7), CD4 (GK1.5),CD1d (1B1), DEC205 (205yekta), CD4 (RM4-5), CD45 (30-F11), CD3 (17A2),F4/80 (BM8), CD11b (Mino), B220 (RA3-6B2), CD8a (53-6.7), IL-12p35(4D10p35), IL-1α (ALF-161), MCH II (M5/1 14.15.2), CD25 (PC61.5)(eBioscience), Ly6G (1a8)(BD Biosciences). Caspase 1 activity wasmeasured by flow cytometry using the FLICA caspase 1 reagent(FAM-YVAD-FMK) (Immunochemistry Technologies). Cells were incubated with7-AAD for viability assessment. Secreted cytokines (IL-1a, CXCLI, CXCL2and IL-12p70) were measured by ELISA (R&D Systems). For cytokinesecretion, murine BMM, prepared as described [Ponpuak, 2010 #13020],were stimulated with 5 ng/ml mIFN-y and 100 μg/ml LPS, with autophagyagonist and antagonists rapamycin (Invivogen), 3-MA, bafilomycin A1, andALLN (Sigma) added 30 minutes prior to LPS and IFN-γ stimulation. Forautophagy-dependent unconventional secretion of cytosolic cytokines asdescribed [Dupont, 2011 #14374], BMM were stimulated for 1 h with 250μg/ml silica (MIN-U-SIL-15, US Silica) with starvation (EBSS) to induceautophagy.

Microscopy and Image Analysis

For confocal microscopy, BMM were stained with mouse anti-GFP (Abeam, 10μg/ml) to enhance LC3-GFP visualization, rabbit anti-caspase 1 (SantaCruz Biotechnology), rabbit anti-calpain 1 (Cell Signaling Technology),or hamster anti-IL-1a (eBioscience) followed by secondary antibodies.Pearson's colocalization coefficients were derived using SLIDEBOOK 5.0(Intelligent Imaging Innovations) applying the SLIDEBOOK 5 defaultalgorithm command ‘AND’. All Pearson's coefficients were derived fromthree independent experiments with five fields or more per experiment,for a total of 15 fields contributing to the cumulative result.

Delayed-Type Hypersensitivity and Cell-Mediated Immunity

Mice were infected intranasally with 5×106 BCG for 21 days, and theninjected with the synthetic PPD (a five antigens cocktail: Dnak, GroEL,Rv009, Rv0569, and Rv0685) at 1.0 μg/ml in PBS, or PBS control, 50 μl inseparate footpads. DTH was assessed as described [Yang, 2011 #14416] bycomparing swelling to a baseline value immediately after injection.Splenocytes (5.0×105 cells/well) were restimulated with the syntheticPPD adjusted for 2.0 μg/ml (Dnak and GroEL), and 4.0 μg/ml (Rv009,Rv0569 and Rv0685) and culture supernatants assayed for IFN-y, TNF-a,IL-4 and IL-17 secretion by ELISA (R&D Systems).

T Cell Assays

Single cell suspensions from whole lungs isolated from naYve Atg5fl/flLysM-Cre+ and Cre− mice were cultured in RPMI 10% FBS and CellStimulation Cocktail (phorbol 12-myristate 13-acetate and ionomycin plusbrefeldin A and monensin; eBioscience) for 4 h and analyzed by flowcytometry. For in vitro polarization, nai″ve CD4+ T cell from spleenswere sorted CD44lowCD4+TCRP+ cells in a MoFlo high speed cell sorter(BeckmanCoulter), sorted cells (5×105 cells/well), incubated withplate-bound anti-CD3 antibody (Hu et al., 2011) and stimulated with 20ng/ml IL-6, 5 ng/ml TGF-p, 20 ng/ml IL-1α or 20 ng/ml IL-I P (R&DSystems) in the presence of anti-CD28 (37.51), anti-IFN-P (R4.6A2),anti-IL-4 (11B1 1), anti-IL-2 (JE56-1A12) (eBioscience). After 4 days,cells were stimulated with Ix Cell Stimulation Cocktail in the presenceof protein transport inhibitors for 5 hours at 37° C. and analyzed byflow cytometry.

Other Experimental Procedures. Additional Methods are Described inSupplementary Materials.

Supplementary Results

Histopathology Findings in Atg5fl/fl LysM-Cre+ Mice Infected with Mtuberculosis H37Rv

At necropsy the veterinary pathologist's findings were as follows: theAtg5-deficient mice exhibited extensive, discreet multinodular tocoalescing foci of lung inflammation (granulomas), whereas the Atg5fl/flLysM-Cre− mice exhibited more subtle lung lesions characterized by mild,patchy foci of white discoloration without nodule formation (FIG. 1B).Microscopic examination revealed that the lungs from the Atg⁵fl/flLysMCre+ mice exhibited marked pulmonary inflammation resembling thecaseating granulomas found in cases of human TB, characterized bynodular, often coalescing foci consisting of peripheral infiltrates oflymphocytes, macrophages, plasma cells and occasional neutrophils,surrounding central foci of necrotic debri containing dead and dyingneutrophils (FIG. 1C; Figure S1D). Acid-fast staining of the lungs fromthese mice revealed abundant intracellular and extracellular bacilli. Incontrast, lungs from the infected Atg⁵fl/fl LysM-Cre− mice exhibitedonly irregular, mild to moderate,

bronchoalveolar and interstitial infiltrates of lymphocytes, macrophagesand plasma cells without organization into discreet nodules. Acid-faststaining of lungs from these mice revealed very sparse intracellularbacilli, and no apparent extracellular bacilli (FIG. 1 C; Figure SIH).

Supplementary Experimental Procedures

M tuberculosis Infection of Atg⁵fl/fl LysM-Cre Mice

M tuberculosis, strain H37Rv, inoculum was prepared by diluting a frozenstock of known titer in sterile PBS/0.05% Tween 80. Mice wereanesthetized with isofluorane (Abbott Laboratories, Chicago, Ill.) and50 μl of fluid containing M tuberculosis were placed on the nostrils ofmice, after which mice were allowed to inhale the inoculum under directobservation. The mice awoke approximately 1 minute after sedation. Themice were kept warm with a heat lamp and allowed to recover under directobservation. One hour after inoculation, 3 randomly selected mice fromthe infected cohort were harvested to determine lung depositions.Bacterial burden was determined using homogenized organs: Samples wereserially diluted and duplicated, and 50 μl aliquots of each dilutionwere spread on Selective Mitchinson 7H1 1 agar plates (Remel) and placedinto humidified incubator at 37° C. for 12 days. Mice were weightedtwice prior to infection on days −3 and −1 for baseline. Upon infection,mice were monitored daily for survival and weighted semi-weekly. At theindicated times, mice were sacrificed by CO2 overdose, and lungs wereharvested and homogenized in 1 ml of PBS/0.05% Tween 80. Forhistopathological examination, lungs were insufflated with 10% neutralbuffered formalin via tracheal cannulation and removed en bloc. At thesame time, spleens were harvested and all organs were placed into 10%buffered formalin for further processing in histological studies.Paraffin embedded sections were stained with hematoxylin and eosin (H&Estain) or acid fast stain and evaluated by a board certified veterinarypathologist. Samples were subjected to a freeze/thaw cycle, sonicatedfor 30 sec, allowed to sit on ice for 30 min, centrifuged at 12,000 rpmfor 10 min, supernatants collected and filtered through a 0.45 μmsyringe filter and assayed for cytokines using the Luminex MultiplexSystem (Luminex Corp, Austin Tex.). Beads for cytokine quantificationwere from Invitrogen and used according to the manufacturer'sinstruction.

Cells and Tissue Preparation

Lungs were perfused with sterile saline in order to remove peripheralblood cells. Lungs were then minced and enzymatically (DNAse/collagenasesolution) treated at 370 C for 60 min. The digested lung tissue was thenmechanically disrupted using a pestle and wire screen. Cells were thenfiltered over a nylon wool column to remove particulate and remainingred blood cells were lysed and cells were then centrifuged through alayer of 30% percoll to remove debris and dead cells. Spleens werehomogenized in HESS containing HEPES, L-glutamine and pen-strep (HGPG)using frosted slides. For lung homogenate, lungs were minced,homogenized, homogenate resuspended in a total volume of 1 ml PBS,pressed through a 70-mm cell strainer, centrifuged and clarifiedsupernatant collected for analysis.

Antibodies, Immunoblotting, Detection Assays, siRNA Knockdowns and FlowCytometry

Cells were washed with PBS and lysed with RIPA buffer containingprotease inhibitor cocktail (Roche). Cells extracts were analyzed bystandard immunoblotting techniques with antibodies to ASC (Enzo LifeScience, AL 177), procaspase-1 and active caspase-1 (P20) (CellSignaling, 2225), GFP (Abeam), calpain I (Cell Signaling), p62 (Abeam)and actin (Sigma). Proteins were resolved on a 12% SDS-polyacrylamidegels and transferred to nitrocellulose membranes. The membrane wasblocked for 1 h in 5% nonfat dried milk in PBS/Tween 20 (0.1%) andprobed with primary antibody overnight at 4° C. After washing withPBS/Tween, the blot was probed with appropriate anti-mouseHRP-conjugated secondary antibody for 1 h at room temperature andstained with SuperSignal West Dura chemiluminescent substrate (ThermoFisher Scientific). Actin was used as standardization control. For siRNAknockdowns, BMM were transfected by nucleoporation using NucleofectorReagent Kit Mouse Macrophage (AmaxalLonza Biosystems). For murine p62 orAtg5 knockdowns, cells were transfected with siGENOME SMARTpool reagents(Dharmacon). p62-(GCATTGAAGTGGATATTGA; GACGATGACTGGACCCATT;TCGGAGGATCCCAGTGTGA; CAGCAAGCCGGGTGGGAAT), Atg5-(CCAAUUGGUUUACUAUUUG;CGAAUUCCAACUUGCUUUA; UUAGUGAGAUAUGGUUUGA; GCAUAAAAGUCAAGUGAUC).Non-targeting siRNA pool (Scramble) was used as acontrol—(UAGCGACUAAACACAUCAA; UAAGGCUAUGAAGAGAUAC; AUGUAUUGGCCUGUAUUAG;AUGAACGUGAAUUGCUCAA).

At 48 h post transfection, cells were stimulated overnight with LPS andIFN-γ (1 μg/ml and 5 ng/ml, respectively) and the supernatants werecollected for further analysis. Cells were collected and analyzed fortargeted protein expression by immunoblotting as described above. Flowcytometry was carried out on a LSRFortessa or FACSCalibur (BDBiosciences) and data analyzed using FlowJo software (TreeStar).

Quantitative RT PCR

Total RNA was isolated from BMM using RNeasy kit (Qiagen) and cDNA wasgenerated using QuantiTect Reverse Transcription kit (Qiagen). RT-PCRwas performed using SYBR Green I QuantiFast SYBR Green Kit (Qiagen)using the following amplification conditions: PCR initial activationstep: 950 C-5 min; Two-step cycling: Denaturation: 950 C-10 sec;Combined annealing/extension: 600 C-10 sec; Number of cycles 40. Theprimers for IL-1a: (F) 5′-GCA ACG GGA AGA TTC TGA AG-3; (R) 5′-TGA CAAACT TCT GCC TGA CG-3′. The results were analyzed using relativequantification by comparing the ratios of the target gene and thereference housekeeping gene, actin.

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Example 2 TBK-1 Controls Autophagy Pathway in Cell-AutonomousAntimicrobial Defense

We screened the Rab family of membrane trafficking regulators foreffects on autophagic elimination of Mycobacterium tuberculosis var.Bovis BCG and found that Rab8b and its downstream effector, innateimmunity regulator TBK-1, are required for autophagic elimination ofmycobacteria in macrophages. TBK-1 was necessary for proper autophagicflux via coordinated assembly and function of the autophagic machinery.TBK-1 phosphorylated the autophagic adaptor p62/sequestosome 1 onSer-403, a residue essential for its role in autophagic clearance. TBK-1was required for the execution of IL-1P-induced autophagy and IL-IP-dependent autophagic killing of mycobacteria. Thus, TBK-1 is a keyregulator of immunological autophagy and is responsible for thematuration of atophagosomes into lytic bactericidal organelles.

We approached the far less studied processes governing autophagic fluxby a systematic screening of Rahs, the central regulators of membranetrafficking and organellar identity in eukaryotic cells (Stenmark,2009). We show that Rab8b and its downstream effector TBK-1 play a keyrole in orchestrating autophagic maturation and cell-autonomous defenseagainst mycobacteria. We furthermore show that the major proinflammatorycytokine IL-1 induces autophagy, that the IL-1-stimulated autophagy caneliminate intracellular Mycobacterium tuberculosis, and that TBK-1 wasresponsible for maturation of autophagosomes into mycobactericidalorganelles. Finally, we show that TBK-1 phosphorylates a key autophagyadapter p62/sequestosome 1 (Bjorkoy et al., 2005), the founding memberof a new subfamily of pattern recognition receptors (PRRs) termedSequestosome: . . . like receptors (SLRs) (Deretic, 2011), at theSer-403 residue essential for its autophagic clearance function.

Results

Rab Screen for Autophagic Killing of M tuberculosis Var. Bovis BCGReveals a Role for Rab8b.

We screened a library of siRNAs to all murine Rahs and Rablike factors(FIG. 1A and Suppl. Table S1) for effects on the previouslycharacterized (Gutierrez et al., 2004; Harris et al., 2007; Singh etal., 2006; Singh et al., 2010) autophagic killing of Mycobacteriumtuberculosis var. bovis BCG (BCG), as a demonstrated (Ponpuak et al.,2010) measure of the function of the entire autophagy pathway (frominitiation to maturation) in a biologically, immunologically, andmedically significant system. The previously implicated endocytic Rahs(e.g. Rab5) showed a role in accordance with observations in otherautophagy-dependent systems (Ravikumar et al., 2008). Additional Rahsdisplayed a range of effects on autophagic killing of BCG, includingthose Rahs previously implicated in autophagy, e.g., Rab7, Rab32,Rab33b, (Hirota and Tanaka, 2009; Itoh et al., 2011; Jager et al., 2004)with the notable exception of Rab2, (Olkkonen et al., 1993). We focusedin subsequent studies on two Rahs, Rab8b and Rab34, which had noimmediately predictable function whereas our preliminary observationsindicated that they affected autophagic maturation.

A knockdown of Rab34 caused premature formation of autolysosomes (Suppl.Fig. SIA) associated with a decline in the ability to kill BCG (Suppl.Fig. SIB), reduced plasma membrane expression of CD98 (Suppl. Fig.SIC-E), a subunit of amino acid transporters that import amino acidsincluding leucine. A knockdown of Rab34 diminished [3H] Leu uptake bythe cells (Suppl. Fig. SIF), and its effects on autophagy measured byLC3-II could be reversed by addition of methyl-pyruvate to the medium(Suppl Fig. SIG). The action of Rab34 was complementary to thepreviously reported effects of Rab? (Edinger et al., 2003) and althoughindirect was informative regarding how cellular energetics governsautophagy in cell-autonomous defense against microbes.

Rab8b knockdown caused a decrease in conversion of BCG phagosomes todegradative compartments following induction of autophagy (Gutierrez etal., 2004; Harris et al., 2007; Ponpuak et al., 2010) (FIG. 1X2B-D) andautophagic killing of mycobacteria (FIG. 1X2E). In side-by-sidecomparisons, we observed only a trend with Rab8a (Suppl. Fig. SIR),whereas Rab8b siRNA reproducibly diminished autophagic killing of BCG ina statistically significant fashion (FIG. 1X2E). We concluded that bothRab8a and Rab8b likely play a role in autophagy but that Rab8b had adominant effect at least in our model system measuring autophagickilling of mycobacteria.

TBK-1 is a Downstream Effector of Rab8b Contributing to AutophagicElimination of Mycobacteria by Affecting Autophagic Maturation.

How might Rab8b affect autophagic killing of mycobacteria? Among the fewknown interacting partners of Rab8b is FIP-2 (also known as optineurin;FIG. 2X2A). FIP-2 in turn associates with the wild type (non-pathogenic)huntingtin (Htt) (Hattula and Peranen, 2000), and TBK-1 (Morton et al.,2008), a protein broadly conserved within Coelomata. TBK-1 is a pivotalregulator of innate immunity strategically positioned at the interfacewith cellular pro-survival pathways (Ou et al., 2011). Htt and TBK-1have been thus far implicated as an autophagic degradation substrate(mutant Htt aggregates (Ravikumar et al., 2008; Sarkar et al., 2007))and, in the case of TBK-1, as being indirectly inhibited byintracellular trafficking imposed by the autophagy factor Atg9 (Saitohet al., 2009) or playing a role in modifying an autophagic adaptor forSalmonella (Wild et al., 2011). Here we considered a model, wherebythese factors could play an active role in the regulation of theautophagic pathway. The role of the wild type Htt is not well understoodalthough it has been implicated in cargo trafficking from thetrans-Golgi network (TGN) to lysosomal compartments (del Toro et al.,2009). We first tested whether the Rab8b phenotype was exerted via Httas a putative effector (known to functionally affect peripheral myeloidcells in Huntington's disease patients (Bjorkqvist et al., 2008)).However, an Htt knockdown in macrophages did not result in astatistically significant loss of autophagic killing of BCG (FIG. 2B).Thus, we concluded that Htt was not critical for autophagic eliminationof mycobacteria and turned our attention to TBK-1.

In contrast to Htt, a knockdown of TBK-1 caused a deficit in autophagickilling of BCG (FIG. 2X2B), indicating that Rab8b effects on autophagyand elimination of mycobacteria may be exerted via TBK-1. This wasconfirmed using the TBK-1 inhibitor BX795 (Clark et al., 2009). Whenmacrophages were treated with BX795, this abrogated starvation-inducedBCG phagosome maturation (FIG. 2X2C) and autophagic killing of BCG (FIG.2X2D).

TBK-1 is Necessary for Autophagosome Maturation.

We next tested how TBK-1 affected autophagy and found that TBK-1knockdown did not affect formation of autophagosomes but suppressedtheir maturation (autophagic flux) into autolysosomes, as revealed bythe tandem RFP-GFP-LC3 reporter (FIG. 2X2E,F), which identifies earlyautophagic organelles as RFP+ GFP+ and matured autolysosomal organellesas RFP+ GFP− since GFP (but not RFP) fluorescence is sensitive tolumenal acidification (Kimura et al., 2007; Pankiv et al., 2007). A lossof TBK-1 reduced the number of RFP+ GFP− acidified autophagic organellesand increased RFP+ GFP+ puncta, consistent with inhibition of autophagicmaturation (FIG. 2 X2E,F). A positive role of TBK-1 in autophagosomalmaturation was confirmed by LC3 immunoblots in TBK-1−/− MEFs (FIG. 2X2G,H). MEFs lacking TBK-1 showed accumulation of LC3-II (a marker ofearly autophagic organelles) under both basal (full medium) and induced(starvation) conditions. The increase in LC3-II in the absence of TBK-1cannot be explained by de-repression of autophagy initiation since thelevels of LC3-II protected from degradation by bafilomycin A1 wereslightly lower in or equal to TBK-1 knockout cells (FIG. 20,H and Suppl.Fig. S2A).

To confirm that the phenotype was due to TBK-1 deficiency, we inhibitedwith BX795 TBK-1 in wild type (TBK-1+/+) MEFs and tested effects ofBX795 on starvation induced autophagy. As with genetically deficientTBK-1−/− MEFs, pharmacological inhibition of TBK-1 led to diminishedautophagic maturation as determined by LC3-II blots (Suppl. Fig. S2B,C).Although attempts to complement the absence of TBK-1 in Tbkl-1-MEFs bytransfection with Tbk-1 expression constructs was hampered by lowtransfection efficiency, overexpresion of Tbk-1 transgene in RAW 264.7cells caused alterations in LC3-II levels, which diminished faster withtime in Tbk-1 transgeneexpressing cells relative to untransfected cells(Suppl. Fig. S2D,E). The LC3-II immunoblot experiments and the assaysusing RFP-GFP-LC3 reporter collectively established that TBK-1 was keyfor autophagic flux and maturation. TBK-1 was also important fordelivery of the lysosomal hydrolase Cathepsin D to autophagolysosomalcompartments, purified from macrophages induced for autophagy bystarvation using magnetic beads as previously described (Ponpuak et al.,2010), as knocking down TBK-1 diminished cathepsin D delivery to onethird of normal (Suppl. Fig. S3A). This was specific for TBK-1 as aknockdown of another Rab8b-optineurin interacting partner, Htt, did notreduce cathepsin: D delivery (Suppl. Fig. S2A). TBK-1 was also neededfor delivery of Cathepsin D to conventional phagolysosomes (Suppl. Fig.S2B) mirroring the Rab8a-dependent delivery of cathepsins from the TGNto the lysosomal compartments (del Toro et al., 2009).

TBK-1 is Necessary for Maturation of IL-IP-Induced Autophagic Organellesand Mycobacterial Killing in Macrophages.

Although IL-IP is a key proinfiammatory cytokine, its role in autophagyhas not been a subject of in-depth studies. It has nevertheless beenindirectly implicated in autophagy during MHC class I presentation ofviral antigens (English et al., 2009) and in studies of autophagyactivation via TLR4 signaling pathways (Shi and Kehrl, 2010). Since IL-1Ws role in cell-autonomous autophagic defense against intracellularpathogens has not been investigated and in order to provide animmunologically relevant context in which to test the role of TBK-1 inautophagy, we examined here whether IL-1P could induce autophagy inmacrophages, whether IL-1P-induced autophagy could inhibit intracellularM tuberculosis, and whether TBK-1 played a role in these processes.

When RAW264.7 macrophages transiently expressing EGFP-LC3 were treatedwith mouse IL-1p this induced LC3 puncta formation (FIG. 3 X2A). WhenRAW264. 7 cells transiently expressing the tandem RFP-GFP-LC3 probe werestimulated with IL-1P (FIG. 3 X2B), an increase in both earlyautophagosomal (R+G+) and mature, acidified puncta (R+G−) was detectedindicating that IL-1p induces both autophagic initiation and maturationresulting in progression through the autophagic pathway. Induction ofautophagy by IL-1p was confirmed by immunoblot analysis of lipidatedLC3-II levels in the presence of autophagic maturation inhibitorbafilomycin A 1, since LC3-II levels were increased in IL-1P-stimulatedcells (FIG. 3 X2C). IL-1p induced autophagy in primary cells, includingmurine bone marrow-derived macrophages (BMM) (Suppl. Fig. S3C) and humanperipheral blood monocyte-derived macrophages (Suppl. Fig. S3D).Induction of autophagy by IL-1p was dependent on MyD88, similarly towhat as been reported for LPS and TLR4, as shown by expression ofdominant negative MyD88 (FIG. 3 X2D) and by analyzing BMM from MyD88knockout mice (FIG. 3E). A progression through the autophagic pathwaywas confirmed by detecting proteolysis of long-lived proteins (Robertsand Deretic, 2008) in macrophages stimulated with IL-1p (FIG. 3 X2F).Finally, we used mycobacterial killing as a measure of autophagiccell-autonomus defense output (Ponpuak et al., 2010). IL-1p inducedkilling of M tuberculosis, whereas elimination of mycobacteria wasabrogated in cells that were knocked down for Atg7 (FIG. 3 X2G),demonstrating that IL-1P-induced autophagy can, similarly to starvation(Ponpuak et al., 2010), eliminate intracellular M tuberculosis.

Having established that IL-1p induces autophagy with its physiologicaland cell-autonomous immunity outputs, we asked whether TBK-1 wasimportant for these processes. RAW264.7 macrophages infected withmycobacteria were stimulated with IL-1P or by starvation in the presenceor absence of TBK-1 inhibitor BX795. Either starvation or IL-1 P causedmycobacterial killing, whereas BX795 abrogated (FIG. 4 X2A) whereasTBK-1 siRNA (FIG. 4 X2B) reduced their autophagic elimination. As withstarvation, TBK-1 inhibition did not affect initiation of autophagy(FIG. 4C,D) but suppressed autophagic maturation (FIG. 4 X2E,F). Inconclusion, TBK-1 is important for conversion of autophagic organellesinto mature and bactericidal organelles, for both physiologically(starvation) and immunologically (IL-1 P) induced autophagy.

TBK-1 Associates with Rab8b and Colocalizes with Rab8b on AutophagicOrganelles.

We next turned to the mechanisms of how TBK-1 affects autophagy.

If Rab8b and TBK-1 cooperate in the control of the autophagic pathway,we reasoned that they might associate. This was tested and shown incoimmunoprecipitation experiments with GFP-Rab8b (FIG. 5A). When weexamined intracellular localization of Rab8b and TBK-1 relative toautophagic organelles, TBK-1 colocalized with endogenous LC3 and Rab8b(FIG. 5 X2B,C). The autophagic adaptor p62/sequestosome 1, recentlydemonstrated to be critical for autophagic killing of M tuberculosis(Ponpuak et al., 2010) also colocalized with TBK-1 (FIG. 5 X2D,E).Supplementary Fig. S4 shows colocalization analyses of TBK-1 and LC3with Rab8b (Suppl. Fig. S4A) and with p62 (Suppl. Fig. S4B), underdifferent conditions: basal, induced autophagy, presence or absence ofbafilomycin A1. The colocalization and a striking similarity in theoverall intracellular organellar distribution were enhanced in thepresence of LC3- and p62-sparing activity of bafilomycin A1 (FIG. 5X2B-E; Suppl. Fig. S4A,B). We conclude that Rab8b and TBK-1 localize toautophagosomal organelles in keeping with their role in regulatingautophagic flux.

Induction of Autophagy Results in Assembly of Membranous CompartmentsContaining Rab8b, TBK-1 and Autophagy Factors.

When subcellular membranous compartments were separated by isopycniccentrifugation in sucrose gradients, induction of autophagy resulted inredistribution of multiple components engaged in autophagy causing themto co-fractionate with TBK-1 and Rab8b (FIG. 6A,B). These were LC3-II,the autophagic adaptors p62/sequestosome 1 (Bjorkoy et al., 2005;Johansen and Lamark, 2011) and NDP52 (Thurston et al., 2009), as well asUVRAGNPS38, the component of the Beclin 1-hVPS34 complex II specific forautophagosomal maturation into lytic compartments (Ling et al., 2008).In keeping with its sucrose gradient cofractionation with TBK-1 (FIG.6A,B), UVRAG colocalized with TBK-1 (FIG. 6 X2C, D). Both autophagicadaptors (Johansen and Lamark, 2011) p62 (Bjorkoy et al., 2005) andNDP52 (Thurston et al., 2009) colocalized with TBK-1 (FIG. 6 X2E-G),congruent with the biochemical analyses of intracellular organellesseparated on sucrose gradients (FIG. 5 X2A-B). In the imagingexperiments in FIG. 6E-G no bafilomycin A1 was added and thus asexpected upon induction of autophagy by starvation, p62-TBK-1 andNDP52-TBK-1 colocalization was reduced (FIG. 6 X2F,G).

These findings expanded the spectrum of autophagic machinery componentsconverging on Rab8b and TBK-1 containing compartments.

TBK-1 Affects p62 Clearance.

If TBK-1 is needed for autophagic maturation, we reasoned that it mightaffect clearance of the autophagic adaptor p62, as it has been reportedto be a good marker of autophagic maturation, matching or exceeding inperformance LC3-based assays (Larsen et al., 2010). Using antibody toendogenous p62 we employed high content quantitative imaging analysisand detected significant increase in p62 puncta in BMMs treated withTBK-1 inhibitor BX795 (FIG. 7 X2A-C). Western blot analysis confirmedthat p62 levels increased when TBK-1 was inhibited (FIG. 7 X2D), inkeeping with the high content image analysis of p62. TBK-1 was alsonecessary to authorize p62/sequestosome 1 for autophagic degradation,since p62/sequestosome 1 accumulated in TBK-1−/− cells; the surplusp62/sequestosome 1 seen in TBK-1−/− MEFs showed a laddering pattern(Suppl. Fig. S5) neither previously reported nor observed here in thepresence of TBK-1. Furthermore, ubiquitinated proteins accumulated inTBK-1−/− cells revealed by pull-down assays in cellular extracts usingTUBE-2 (tandem ubiquitin binding entities 2), which recognizespolyubiquitinated proteins and protects them from deubiquitinatingenzymes and proteasome during isolation (Hjerpe et al., 2009) (FIG. 7X2E) This indicates that p62 is not being cleared by autophagy whenTBK-1 is unavailable and accumulates in the cell, that TBK-1 is neededto enable p62's entry into autophagic degradative pathway, and thatseveral ubiquitinated cargo do not enter degradative pathways in theabsence of TBK-1.

TBK-1Phosphorylates p62 on Ser-403.

To determine whether TBK-1 modified (e.g. phosphorylate) p62 in vivo andto examine the potential sites involved we co-expressed GFP-p62D69A(mutant preventing oligomerization of p62) and myc-TBK 1 in HEK293cells, immunoprecipitated GFP-p62 from cellular extracts and carried outmass spectrometry analyses on the immunoprecipitated material. As acontrol, we cotransfected GFP-p62D69A with myc-TBK-1K38D, a kinasedefective mutant. By manual inspection of the mass spectrometry data, apeptide of 857.01 m/z (2568.03 Da) was detected in GFP-p62D69Aexpressing cells cotransfected with myc-TBK-1, but not when GFP-p62D69Awas co-expressed with the kinase defective mutant myc-TBK-1K38D (FIG. 7X2F). The 857.01 m/z (2568.03 Da) peptide was selected for tandem massspectrometry and identified as the LIESLSQMLpSMGFSDEGGWLTRphosphopeptide from p62, where serine 403 in the UBA domain of p62 isphosphorylated (FIG. 7 X2G,H). The unphosphorylated peptide with themass 2488.1 was observed in both samples. The Ser-403 site correspondsto the TBK-1 consensus sequence SxxxpS. Thus, TBK-1 affects p62phosphorylation of the ubiquitin associated (UBA) domain, providing aspecific link between TBK-1 and autophagic adaptor posttranslationalmodifications. A recent study (Matsumoto et al., 2011) has shown thatphosphorylation of Ser-403 strongly increases affinity of the UBA domainof p62 for K48 and K63-linked ubiquitin chains, and promotes autophagicclearance of p62 and polyubiquitinated protein aggregates. Using aphosphospecific antibody developed by Matsumoto et al., (2011), wemonitored phosphorylation of Ser-403 in vivo and in vitro (FIG. 7X2I,J). TBK-1 phosphorylated Ser-403 of endogenous p62 in HEK293 cellstransfected with a mycTBK-1 expression vector (FIG. 7 X2I). This was notobserved when HEK293 cells were transfected with kinase defective TBK-1or when mycTBK-1 expressing cells where treated with the TBK-1 inhibitorBX795 (FIG. 7 X2I). When purified proteins were examined in aphosphorylation in vitro assay, TBK-1 directly phosphorylated p62 at theSer-403 site (FIG. 7 X2J). Thus, TBK-1 phosphorylates p62 at Ser-403, aresidue required for autophagic function of p62 (Matsumoto et al.,2011).

Discussion

This study has uncovered roles of TBK-1 at a specific execution stage ofthe autophagic pathway known as autophagic maturation, and inposttranslational modification of the prototypical SLR (Deretic, 2011),p62, at the Ser-403 residue, known to be essential for its function inautophagic clearance (Matsumoto et al., 2011). Whereas efforts have beendevoted to the initiation and elongation stages of autophagy (Tooze andYoshimori, 2010), the control of the flux and conversion of autophagicorganelles into degradative compartments is just as important since inmost cases autophagy exerts its physiological and immunologicalfunctions by degrading or processing the captured intracellularmaterial. TBK-1 (McWhirter et al., 2004) is a member of the IKK familyof central regulators of innate immunity (Perkins, 2007; Richmond, 2002;Shen and Hahn, 2011) and is a downstream effector of Rab8b. TBK-1 andRab8b are found in shared protein complexes, and following induction ofautophagy, TBK-1 and Rab8b colocalize and cofractionate with autophagicorganelles. TBK-1 is required for the execution of the maturationprogram and autophagic killing of mycobacteria in response tophysiological (starvation) and immunological (IL-1 P) stimuli.Furthermore, TBK-1 phosphorylates the key Ser-403 residue ofp62/sequestosome 1, an autophagic adaptor (Bjorkoy et al., 2005) that isthe founding member of the new class of innate immunity receptors termedSLRs (Deretic, 2011). The phorphorylation of Ser-403 on p62 enables thisPRR to recognize and autophagically clear target substrates (Matsumotoet al., 2011).

TBK-1 enables the execution of autophagosomal maturation and likelycouples this stage of autophagy with cargo capture. This is evidenced bythe in vivo dependence on TBK-1 of the phosphorylation of the keySer-403 residue within the UBA domain of one of the principal autophagicadaptors, p62/seqestosome 1. While our study was in revision,phosphorylation of Ser-403 by CK2 was shown to increase affinity of p62UBA for polyubiquitin chains on its cargo (Matsumoto et al., 2011). Ourfindings are congruent with these observations and suggest that TBK-1also targets and phosphorylates directly the Ser-403 site, thus linkingimmunological and physiological inputs with p62 UBA activation in vivo.Of further note is that our data on the effects of TBK-1 on autophagicmaturation are in keeping with the extended model recently depicted byvon Muhlinen et al., (von Muhlinen et al., 2010), whereby TBK-1 plays arole not only in modifying autophagic adaptors such as NDP52 (Thurstonet al., 2009), optineurin (Wild et al., 2011), and as shown here p62,but also plays additional but hitherto undefined roles in the autophagicpathway.

The Rab screen performed here relied on the cell-autonomousantimicrobial defense functionality that depended on the execution ofthe entire autophagic pathway as previously defined (Ponpuak et al.,2010) from signaling and initiation, through maturation, to its finalbiological output, i.e. the bactericidal action of autophagy. Weacknowledge that this approach may not account for functions of Rahs inthe context of how starvation may affect viability of mycobacteria by apotentially unknown process other than autophagy. In this work, wefocused on two Rahs, Rab34 and Rab8b, which have not been covered inprior studies. Of the two Rab8 GTPases only Rab8b showed statisticallysignificant effect on autophagic killing of BCG. Although Rab8a andRab8b share several interacting partners, Rab8b also features a numberof unique interactors (Chen et al., 2001; Fransen et al., 2008; Heidrychet al., 2008) and the Rab8b sequence diverges from Rab8a in its variableregion near the C-terminus. Since optineruin binds Rab8a as well asRab8b, it is likely that differences in localization of Rab8b-optineurinunderlie the stronger Rab8b engagement with autophagy maturation asdetected here, along with potential participation of unique interactingpartners specific for Rab8b, e.g. otoferlin, associated with autosomalrecessive deafness (Heidrych et al., 2008), and Pex5Rp/TRP8b, a proteinrelated to the peroxisomal targeting signal 1 receptor Pex5p (Fransen etal., 2008). The other Rab8 paralog, Rab8a, does associate with a subsetof LC3 compartments, however they specialize in the alternativesecretory pathway of inflammasome substrates such as IL-1p (Dupont etal., 2011).

The follow up analyses with Rab34 led to a connection with amino acidimport. This is a plausible link since autophagy is controlled by aminoacid starvation and can be abrogated by addition of amino acids such asleucine (Grinde and Seglen, 1981). Cells displayed reduced leucineuptake when Rab34 was knocked down and thus the negative effects of theloss of Rab34 on autophagic killing of BCG may appear paradoxical.However, a similar effect was observed in studies with myotubularins(Vergne et al., 2009) where knocking down myotubularinphosphatidylinositol 3-phosphatases led to chronic autophagy activationand exhaustion, diminishing its efficacy in antimicrobial defense. Theseobservations underscore a requirement for precise timing of autophagyinduction in order for it to exert its cell-autonomous antimicrobialdefense. Since autophagy is affected by growth factors and hormones(Ezaki et al., 2011) its response to immunological signals (Delgado etal., 2008; Gutierrez et al., 2004; Harris et al., 2007; Shi and Kehrl,2010; Tang et al., 2010; Xu et al., 2007), nutritional and hormonalimbalance may be a determinant of the efficacy of autophagicimmunological outputs.

TBK-1 is spatially and biochemically associated with Rab8b in thecontext of autophagy, and this likely occurs via an intermediary proteinoptienurin. Optineurin mutants with altered binding of TBK-1 have beenlinked to glaucoma (Morton et al., 2008) whereas optineurin mutationslinked to amyotrophic lateral sclerosis (ALS) display changes ininflammatory signaling (Maruyama et al., 2010). Optineurin is present inneuronal cytoplasmic inclusions in ASL and in a range ofneurodegenerative disorders (Maruyama et al., 2010; Osawa et al., 2011).Given the neuroprotective role of autophagy (Mizushima et al., 2008),optienurin's mechanism of action in disease may now be considered in thecontext of autophagy. Optineurin, also known as NEMO-related protein(NRP) is a tetra-ubiquitin binding protein (Laplantine et al., 2009).NEMO (or IKK-y) is a regulatory scaffold for IKK-a and IKK-P (canonicalIKKs), controlling proinflammatory responses via NF-KB, whereasoptineurin serves as a platform for assembly of multiprotein complexesincluding TBK-1 (Morton et al., 2008). TBK-1 is in turn linked to theautophagic adaptor NDP52 (Thurston et al., 2009) via Sinbad and Nap 1,in keeping with our observations that induction of autophagy bystarvation leads to co-fractionation of TBK1 and NDP52. The two(canonical IKK and TBK 1) platforms show more interactions thanpreviously appreciated (Clark et al., 2011), which opens the possibilityof a sequential or coordinated action in autophagy of canonical IKKs(Comb et al., 2011; Criollo et al., 2010) and TBK-1 as revealed here.

TBK-1 turned out to be important in cell-autonomous defense againstmycobacteria downstream of macrophage activation by inflammatorycytokine IL-1p. We show in this study that IL-1 P induces autophagy in aMyD88-dependent fashion and that one of the outputs of thisproinflammatory cytokine is to promote autophagic killing of Mtuberculosis. This is in keeping with the reports that IL-1 P, IL-1R,and MyD88 are important in elimination of M tuberculosis (Fremond etal., 2007; Master et al., 2008; Mayer-Barber et al., 2010). Congruentwith our observations, IL-1p has been indirectly implicated in previousstudies investigating immunological roles of autophagy (English et al.,2009; Shi and Kehrl, 2010). IL-1 P thus joins other alarmins, such asHmGm (Tang et al., 2010), as an inducer of autophagy. On the flip side,autophagy-based unconventional secretion has been implicated inactivation and extracellular delivery of IL-1p and HMGB1 (Dupont et al.,2011), thus indicating a possible role for autophagy in amplifyingautocrine and paracrine signals of key alarmins IL-IP and HMGB-1.Whether TBK-I primarily plays a role in promoting autophagic flux duringIL-1β- or starvation-induced autophagy that has been uncovered in ourpresent study, or also throttles autophagy-based unconventionalsecretion remains to be determined.

A further connection between TBK-1, autophagy, and immunologicalfunctions has been recently suggested by implicating TBK-1 viaoptineurinsponsored events in autophagic control of Salmonella when itescapes in the cytosol (Wild et al., 2011). Both the study by Wild etal., (Wild et al., 2011) and our present work are in keeping with thereport by O'Riordan and colleagues (Radtke et al., 2007) uncovering therole of TBK-1 in control of intracellular bacteria, in addition to itswell appreciated role in antiviral defenses. O'Riordan and colleagues(Radtke et al., 2007) pointed to the role of TBK-1 as keeping thecytosolic bacteria in check by a mechanism that at the time wascharacterized as prevention of bacterial escape into or multiplicationin the cytosol but was deemed not to involve autophagy due to anapparent increase in LC3 puncta in Tbk-1−/− cells. Given that TBK-1, asshown here, is primarily involved in autophagosomal maturation,accumulation of LC3 in the absence of TBK1 observed by O'Riordan (Radtkeet al., 2007) and colleagues remarkably fits our data showing that TBK 1controls flux and progression through the autophagic pathway (causingdisappearance of the initially formed LC3 puncta via degradation inautolysosomes), rather than its initiation (characterized by appearanceof LC3 puncta). Thus, all presently existing data are compatible withthe role of TBK-1 in autophagic maturation and its role as anantimicrobial mechanism that can eliminate cytoplasmic bacteria.

The role of TBK-1 in autophagy maturation expands the role of 1KKs inautophagy, previously limited to IKK-a and IKK-P (Comb et al., 2011;Criollo et al., 2010). IKK-a and IKK-P, play a role in the induction ofautophagy (independently of NF-K13) in response to starvation (Comb etal., 2011; Criollo et al., 2010). We propose a model in which IKK-a andIKK-P serve to initiate autophagy whereas TBK-1 ensures its completion.Nevertheless, a recent report (Clark et al., 2011) has indicated anegative regulatory interaction between the canonical IKKs (IKK-a andIKK-P), and IKK-related factors (TBK-1 and IKK-E/i). This poses thequestion of potential antagonism between the canonical IKKs and TBK-1and IKK-E/i.

We however did not observe a negative effect of TBK-1 on autophagyinitiation since LC3-II levels were equal or reduced (and not increased)in Tbk−/− MEFs when the autophagic flux was blocked using bafilomycinA1. Nevertheless, at least one self-limiting feed-back loop exists at adifferent level in the TBK-1-autophagy system, based on the reportednegative regulatory effects of several Atg factors on TBK-1 signaling(Jounai et al., 2007; Saitoh et al., 2009).

In sum, our work has expanded the role in autophagy of IKKs, the centralkinases governing innate immunity, from participation of canonical IKKfamily members in autophagy induction (Comb et al., 2011; Criollo etal., 2010) to now include TBK-1 in the control of autophagic maturationand cell autonomous antimicrobial defense functions of autophagy. Thus,both canonical and non-canonical IKKs play key roles in inflammatorysignaling and cell-autonomous defenses, and our observations and thoseof others may help integrate the role of different IKKs incell-autonomous defenses specifically in the context of autophagy as aninnate immunity mechanism.

Experimental Procedures

Cell Culture, Pharmacological and Cytokine Treatments, Transfections,siRNA Knockdowns, Autophagy Induction, and Immunoprecipitation.

Mouse macrophage-like cell line RAW 264.7 were from ATCC. Tbk-1−/− andTbk-1+/+(wild type) MEFs were from M. O'Riordan, University of Michigan.Murine primary bone marrow macrophages were isolated and differentiatedfrom mouse femur marrows. When indicated, cells were treated with 100 nMbafilomycin A1 to prevent protein degradation in lytic compartments.Cells were treated for 16 h with 10 nM TBKI pharmacological inhibitor,BX795 (InvivoGen). Murine macrophages were treated with mouse IL-I P(Sigma and R&D Biosciences) 50 ng/ml for 16 h or 200 ng/ml for 3 h. RAW2643 cells were transfected by nucleoporation using Nucleofector ReagentKit V (Amaxa/Lonza biosystems). Rahs and Rab-like factors knockdownsdetails are given in Suppl. Table S1). For murine TBK-1 and Huntingtinknockdowns, cells were transfected with SMART pool reagents (Dharmacon).TBK-1 SMARTpool: (GAAGCCGUCUGGUGCAAUA; UGACGGCGCAUAAGAUUUA;CUACGAAGGACGACGCUUA; GUAUGAAG-CGUUUAAAGAU). Huntingtin SMARTpool:(GAAAUUAAGGUUCUGUUGA; CCACUCACGCCAACUAUAA; GAUGAAGGCUUUCGAGUCG;UAACAUGGC-UCAUUGUGAA). Non-targeting siRNA pool (Scrambled) was used asa control. With Rab8's, Rab34, and Rab8 effectors individual orcombinations of two siRNAs from the SMARTpool were used in separateexperiments to establish SMARTpool specificity; in no case were offtarget effects seen within a set of targets examined in this study. Forautophagy effects, cells were uninduced (in full medium) or induced forautophagy by starvation with EBSS for 90 mM (parallel controls withBeclin 1 or Atg7 knockdowns were used to ascertain autophagyauthenticity). Immunoprecipitation was carried out as previouslydescribed (Ponpuak et al., 2010; Singh et al., 2010). An untagged TBK-1cDNA expression construct was from OriGene (vector: pCMV6-XL5).

Subcellular Fractionation, Immunoblot Analysis, Antibodies, and StableProtein Turn-Over.

Subcellular compartments were separated by isopycnic density equilibriumcentrifugation in sucrose gradients as described (Singh et al., 2010).Cells were homogenized in 250 mM sucrose, 20 mM HEPES-NaOH and 0.5 mMEGTA, pH 7.5 (SHE). The post nuclear supernatant was layered on top of apre-formed sucrose gradient consisting of 60%, 50%, 40%, 35%, 30%, 25%,20%, 15% sucrose from top to bottom. The sample was centrifuged at100,000 g in a Beckman SW 40 rotor at 4° C. for 18 hours. Equivalentdensity fractions (verified for refractive index match) were analyzedwith antibodies to UVRAG (MBL), TBK-1 (AbCam), NDP52 (Millipore), LC3(Sigma), p62 (Promega) and Rab8b (custom made); staining was revealedwith Super Signal West Dura chemiluminescent substrate (Pierce).Long-lived protein turnover was measured as described previously(Ponpuak et al., 2009). Anti-phospho-S403 p62 antibody (Matsumoto etal., 2011) was from Nobuyuki Nukina.

Phosphorylation Analysis of p62.

HEK293 cells were transfected using Metafectene Pro (Biontex) withGFP-p62 D69A (a mutant in the PB 1 domain, to prevent oligomerization)and myc-TBK-1 or as a control TBK-1 kinase defective mutant myc-TBK-1K38D. Immunoprecipitation of GFP-p62 D69A from cell extracts preparedfrom two 10-cm plates) using a custom made GFP antibody was performed asdescribed previously (Lamark et al., 2003). Following SDS PAGE, gelbands containing GFP-p62(D69A) were excised and subjected to ingelreduction, alkylation, and tryptic digestion using 2-10 ng/μl trypsin(V511A; Promega) (Shevchenko et al., 1996). Peptide mixtures containing0.1% formic acid were loaded onto a nanoACQUITY UltraPerformance LC(Waters), containing a 5-nm Symmetry C18 Trap column (180 μm×20 mm;Waters) in front of a 1.7-nm BEH130 C18 analytical column (100 μm×100mm; Waters). Peptides were separated with a gradient of 5-95%acetonitrile, 0.1% formic acid, with a flow of 0.4 μI/min eluted to aQ-TOF Ultima mass spectrometer (Micromass/Waters). Each sample was runin ms and data dependent tandem ins mode. Peak lists were generated fromMS/MS by the ProteinLynx Global server software (version 2.2; Waters).The resulting pk1 files were searched against the Swiss-Prat 57.15protein sequence databases using an in-house Mascot server (MatrixSciences). Peptide mass tolerances used in the search were 100 ppm, andfragment mass tolerance was 0.1 Da. Mascot analysis confirmed that thesample contained p62. The Mascot analysis also confirmed that p62 wasphosphorylated on Serine 403 after cotransfection with myc-TBK1. For invitro kinase assays recombinant maltose binding protein (MBP) and MBPp62proteins were purified from E. coli. Recombinant TBK-1 (50 ng;Millipore) was incubated with recombinant MBP, MBP-p62 or MBP-p62 S403Ain the presence of 10 mM ATP and 5 mCi [y-32P]ATP using kinase buffer(40 mM Tris-HCl pH 7.5, 10 mM MgCl2, 1 mM DTT supplemented withCalbiochem phosphatase inhibitor cocktail set II) at 30° C. The reactionwas terminated by boiling in SDS sample buffer after 10 mM. Samples wereseparated by SDS-PAGE, the gels were stained with coomassie brilliantblue, dried and analysed by autoradiography.

TUBE2 Pulldown.

Tandem ubiquitin binding entities (TUBE) in the form of TUBE2-agarosebeads (Lifesensors) were used as described (Hjerpe et al., 2009) to pulldown polyubiquitinated proteins from cell lysates precleared withagarose beads for 1 h at 4° C. and incubated with 20 μl ofpre-equilibrated TUBE2-agarose beads in 20 mM Tris, pH 8.0, 0.15M NaCl,0.1% Tween-20 (TBS-T) with nutation overnight at 4° C. Agarose beadswere washed three times with TBS-T, eluted with 25 μl 2× Laemmeli bufferand subjected to SDS PAGE and immunoblot analysis.

Confocal and High Content Quantitative Microscopy.

Images using a Zeiss LSM 510 Meta confocal microscope (laser wavelength,488 nm, 543 nm and 633 nm). Antibodies against endogenous proteins TBK-1(AbCam), Rab8b (AbCam & custom made), p62 (AbCam), NDP52 (Millipore),LC3 (Sigma) and UVRAG (MBL) were used for indirect immunofluorescenceanalysis. Post-imaging analyses were done with LSM 510 software andSlide Book 5.0 (Intelligent Imaging Innovations) for morphometrics. Forquantitative p62 puncta analysis, Cellomics Array Scan (ThermoScientific) was used to acquire images by computer-driven collection of49 valid fields per well with cells in 96 well plates stained forendogenous p62, and data morphometrically and statistically analyzedusing puncta-counting application within the iDev software (ThermoScientific).

Mycobacterial Survival, Phagosome and Phagolysosome PurificationPurification.

Microbiological analyses of bacterial viability were carried out aspreviously described (Gutierrez et al., 2004; Harris et al., 2007; Singhet al., 2006; Singh et al., 2010) using previously described detailedmethods (Ponpuak et al., 2010; Ponpuak et al., 2009). RAW 264.7 cellswere used to isolate phagosomes (Fratti et al., 2001) or magnetic beadautophagolysosomes (Ponpuak et al., 2010) as previously described.

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Example 3 Autophagy-Based Unconventional Secretory Pathway forExtracellular Delivery of IL-1b

Here, we have addressed the question of whether autophagy plays a directrole in inflammasome and IL-I p activation and secretion. We found that,whereas basal autophagy inhibits IL-1b secretion in concordance with therecent reports (Nakahira et al, 2010; Zhou et al, 2011), inducedautophagy augments IL-1b secretion. We show that inflammasome and theautophagy apparatus synergize during IL-I p secretion in cellsstimulated to undergo autophagy. We also show that autophagy inductioncooperates with GRASP and Rab8a (a GTPase controlling post-Golgipolarized sorting and exocytosis) in driving IL-I P secretion. We, thus,define one of the first biogenesis functions of autophagy in mammaliancells and show that at least one type of unconventional secretionutilizes autophagic machinery in higher vertebrate cells.

Results Induction of Autophagy Promotes Injlammasomedependent IL-1/3Secretion

Whereas it has been found that basal autophagy reduces extracellularrelease of the major proinflammatory cytokine IL-1 P (Nakahira et al,2010; Zhou et al, 2011), we detected the opposite when autophagy wasinduced in primarymurine bone marrow-derived macrophages (BMMs; FIG. 1).Stimulation of autophagy by starvation strongly enhanced IL-1β secretionin response to conventional NLRP3 (NALP3) inflammasome agonist nigericin(FIG. 1X3A). This effect was also seen (FIG. 1B) in western blots ofcaspase 1 and mature IL-1 P of culture supernatants from cells grown inthe absence of serum, as conventionally done when assessing IL-1 Psecretion by immunoblotting (Martinon et al, 2006). A reduced secretionin BMMs from Atg⁵fl/fl LyzM-Crep mice, compared with BMMs from theirCre-littermates, was accompanied and contrasted by the higher level ofcell-associated pro-IL-1 p in Cre− versus Cre+ BMMs (FIG. 1X3B). TheBMMs derived from Atg⁵fl/fl LyzM-Cre+ mice for these and otherexperiments had, as expected, no detectable Atg5 (since the Atg5 gene isexcised in Cre+ macrophages; Zhao et al, 2008) and LC3-II, a key markerof autophagy (Supplementary FIG. S1AX3). The effects of inducedautophagy on secretion of inflammasome substrates described above werenot limited to IL-1b, since secretion of another inflammasome-dependentcytokine from the IL-1 family, IL-18 (IL-1F4), was enhanced whenautophagy was induced (FIG. 1X3C). Pharmacological induction ofautophagy by mTOR inhibition with pp242 (Torkinib) increased secretionof IL-1 P by BMMs (Supplementary Figure S1BX3). An enhancement of IL-1 Psecretion upon induction of autophagy was also detected when particulateinflammasome agonists, alum (Eisenbarth et al, 2008; FIG. 1D;Supplementary Figure S1CX3), silica (FIG. 1E; Hornung et al, 2008), andamyloid-b fibrils (Halle et al, 2008; Supplementary Figure S1DX3), wereused as inflammasome inducers. The enhancement of IL-1p secretionassociated with autophagy induction was inflammasome dependent, as IL-1pactivation was diminished by knockdowns of the inflammasome componentsASC and NLRP3, regardless of whether the inflammasome agonist used wasnigericin or silica (FIG. 1F-HX3). The knockdowns of ASC and NLRP3 didnot change IL-1 P expression (Supplementary Figure SIE and F). Theincreased secretion of IL-1p was not due to the increased cell death ornonspecific membrane permeability as LDH release showed a kinetic lagbehind release of IL-1p whether the inflammasome agonist used wasnigericin or silica (Supplementary Figure S2A-DX3). The stimulation ofautophagy promoted IL-1p secretion in an Atg5-dependent manner, based oncomparisons between BMMs from Atg⁵fl/fl-LyzM-Crep mice and BMMs fromtheir Atg5-competent (Atg⁵fl/fl Cre−) littermates (FIG. 1AX3). However,the loss was not complete in Crep BMMs (FIG. 1AX3). We interpret theincomplete reduction in IL-1 P secretion in the absence of Atg5 as a netresult of two opposing effects-one described here as a product ofpositive contribution of induced autophagy on extracellular delivery ofIL-1p and the other being the recently reported negative regulation ofIL-1 P secretion by basal autophagy (Nakahira et al, 2010; Harris et al,2011; Zhou et al, 2011). In keeping with this interpretation and incontrast to the stimulatory effects of induced autophagy (FIG. 1A-EX3;Supplementary Figure SIB-DX3), basal autophagy negatively affected IL-IP and IL-18 secretion (Supplementary Figure S2E and FX3) in agreementwith the recent reports in cells not induced for autophagy (Nakahira etal, 2010; Harris et al, 2011; Zhou et al, 2011).

IL-1/J and Autophagic Protein LC3 Colocalize in the Cytoplasm

How might induced autophagy enhance IL-1 P secretion? We considered amodel in which autophagy, as a process that can translocate cytosolicproteins and other targets (en masse or specific components) from thecytosol to the inside of vesicular compartments, brought IL-I P into thelumen of autophagic vacuoles followed by exocytosis. When we examinedIL-1p and the key marker of autophagosomes LC3 by immunofluorescenceconfocal microscopy, LC3 and IL-1p colocalized and displayed majorsimilarities in the overall intracellular organellar distribution (FIG.1I-LX3). The overlap between IL-I P and LC3 remained detectable whencells were treated with nigericin (Supplementary Figure S3A-CX3). Theseobservations indicate that autophagic organelles and IL-P intersect.

Inhibition of Autophagyflux Reduces IL-1/J Secretion

A question arose whether the LC3+ organelles containing IL-1P are onpathway to degradation or facilitated IL-1 P secretion. We first testedthe effects of bafilomycin A1, a conventional inhibitor of autophagicmaturation, which acts as an antagonist of vacuolar H+ ATPase andprevents lumenal acidification and autophagosomal cargo degradation. Ifinduction of autophagy acted to degrade IL-I P, then bafilomycin A1 wasexpected to increase IL-1P levels. Instead, bafilomycin A 1 decreasedIL-1p secretion in cells stimulated for autophagy by starvation, whereasno change was observed with bafilomycin A1 in cells undergoing basalautophagy only (FIG. 2AX3).Thus, autophagy flux during autophagy induction was not inhibitory toIL-1P but was instead promoting IL-1p secretion. A similar trend wasdetected with another inflammasome substrate IL-18 (FIG. 2BX3).Equivalent relationships have been observed for IL-I P secretion whethernigericin (FIG. 2AX3) or silica (FIG. 2CX3) was used as inflammasomeagonists. The absence of IL-1 P or IL-18 sparing effects of bafilornycinA1 is in keeping with the interpretation that autophagy is not degradinginflammasome components but that an unobstructed autophagy pathway isnecessary for inflammasome-dependent IL-1 family members secretion.

Lysosomal Hydrolase Cathepsin B is a Positive Factor in Autophagy-DrivenIL-JP Secretion

Next, we investigated the role of lysosomal hydrolases, focusing oncathepsin B. We observed that IL-I P and LC3 colocalized with cathepsinB (FIG. 2DX3 and FIG. 2EX3). However, cathepsin B did not play aninhibitory role. Similarly to bafilomycin A1, cathepsin B inhibitorCA-074 Me suppressed IL-1p production. Instead of protecting IL-1β frompotential degradation, CA-074 Me strongly inhibited IL-1p secretion incells stimulated for autophagy by starvation (FIG. 2FX3). No differencesin expression of pro-IL-I P were observed in cells treated withbafilomyci,n A1 or CA-074 Me (Supplementary Figure S3DX3). Of furtherinterest was that cathepsin B (mature form) was secreted along with theinflammasome substrates in a manner dependent on an intact autophagicapparatus: loss of Atg5 in BMMs from Crep mice (Atg⁵fl/fl LyzM-Cre)diminished the levels of the secreted mature cathepsin B relative toBMMs from Cre⁻ litterrnates (FIG. 2G). The findings with cathepsin 13inhibitor CA-074 Me indicate a positive role for cathepsin B in IL-1pactivation and autophagy-driven pathway of extracellular delivery ofIL-1b. They can also help explain in part the observations that alysosomal hydrolase, cathepsin B, assists in inflammasome activation andIL-1β secretion in response to particulate inflammasome agonists (Halleet al, 2008; Hornung et al, 2008).Rab8a, a Regulator of Polarized Sorting Toplasma Membrane Colocalizeswith IL-JP and LC3 and Controls IL-JP SecretionWe next addressed the features of the compartment where LC3 and IL-I Pcolocalized. We observed an overlap between the LC3+IL-1b+ profiles andRab8a (FIG. 3A-CX3). Rab8a is a regulator of polarized membranetrafficking, constitutive biosynthetic trafficking, and plasma membranefusion of insulin-responsive (Sun et al, 2010) and other vesicularcarriers (Moritz et al, 2001; Bravo-Cordero et al, 2007; Nachury et al,2007; Bryant et al, 2010). Rab8a also colocalized with LC3 and IL-1β incells exposed to nigericin (Supplementary Figure S4A-:-CX3). Rab8a wasrequired for enhanced IL-I P secretion caused by starvation-inducedautophagy and inflammasome activation with nigericin, since siRNAknockdown of Rab8a diminished IL-I P secretion from BMMs under theseconditions (FIG. 3DX3 and (FIG. 3EX3). Rab8a knockdown did not changepro-IL-I P mRNA levels (Supplementary Figure S4DX3). Overexpression ofdominantnegative Rab8a mutant (S22N) inhibited IL-I P secretion fromRAW264.7 cells, employed in that experiment based on their highefficiency of transfection (FIG. 3FX3) (verified by flow cytometry ofGFP-Rab8a for equal yields). Additionally, LC3+ IL-1b+ profiles werepositive for subunits of the exocyst complex (Supplementary FigureS4E-JX3). Exocyst has been shown to cooperate with Rab8a in polarizedplasma membrane delivery of vesicular carriers (Mazelova et al, 2009;Bryant et al, 2010). The presence of exocyst components on IL-1b+autophagic organelles was also in keeping with a recent reportimplicating exocyst in autophagy (Bodemann et al, 2011). In summary,these experiments indicate that systems involved in vectorial vesiculartransport to the plasma membrane participate in autophagy-basedunconventional secretion and that Rab8a is required for efficientautophagy-dependent secretion of IL-1 p.

GRASP55 Controls Secretion of IL-1/J

Two studies in yeast (Duran et al, 2010; Manjithaya et al, 2010) havereported that autophagic machinery is required for unconventionalsecretion of the protein Acb1, and that this pathway depends on theyeast equivalent of a Golgi-associated protein GRASP in mammals (Kinsethet al, 2007; Nickel and Rabouille, 2009). Mammalian cells encode twoGRASP paralogues, GRASP55 (GORASP2) and GRASP65 (GORASP1) (Barr et al,1997; Shorter et al, 1999). We first tested whether any of the mammalianGRASPs were required for IL-I P secretion. We could not obtain a goodknockdown of GRASP65 (GORASP1) and thus could not evaluate itsinvolvement. However, a knockdown of GRASP55 diminished IL-I P secretion(FIG. 4AX3; Supplementary Figure S5AX3). A similar downregulation ofIL-18 secretion was observed with GRASP55 knockdown (SupplementaryFigure S5BX3). We next tested whether GRASP55 showed any detectableresponse to inflammasome stimulation. GRASP55 in resting cells is mostlylocalized aligned within the perinuclear Golgi (FIG. 4BX3; SupplementaryFigure S6AX3). However, a fraction of it dispersed upon treatment ofcells with the inflammasome agonist nigericin (Figure S6BX3) and wasfound juxtaposed and partially overlapping with LC3 profiles (FIGS. 4Band C). Thus, GRASP55 responds to inflammasome stimulation and isimportant for secretion of the inflammasome substrates IL-1 and IL-18.

GRASP55 Controls Autophagy Initiation

In addition to being required for IL-1 secretion, GRASP55 showedfunctional effects on LC3 and autophagy, tested by employing two coreassays (Mizushima et al, 2010): LC3-II lipidation and the RFP-GFP-LC3tandem probe. When GRASP55 was knocked down, autophagy initiation wasnegatively affected, as LC3-II levels were lower in both untreated andbafilomycin A1-treated cells (FIG. 5AX3 and BX3). A partialdownregulation of GRASP65 (to the extent that it could be achieved inBMMs) suggested aminor synergistic effect with GRASP55 on LC3-II levelsupon induction of autophagy (Supplementary Figure S5CX3). Knocking downGRASP55 reduced the total number of autophagic puncta, and selectivelyreduced the formation of autophagosomes but not their maturation (FIG.5CX3 and DX3). This was apparent from the data obtained with theRFP-GFP-LC3 probe following published methods (Kimura et al, 2007),which showed reduced GFP+RFP+LC3 profiles (early autophagosome) andequal number of GFP IU′P+LC3 profiles (mature autophagic organelles) incells knocked down for GRASP55 (FIG. 5DX3). Thus, mammalian GRASP55, aparalogue of GRASP from lower organisms that has thus far been the soledefinitive molecular factor associated with unconventional secretion(Giuliani et al, 2011), displays important and previously unappreciatedpositive regulatory effects on autophagy induction. These findingsstrengthen the connections between autophagy and GRASPs in general, andspecifically demonstrate the role of mammalian GRASP55 both in autophagysubstrates such as IL-1 and IL-18.

Autophagy-Based Unconventional Secretion is not LimitedToproteolytically Processed Inflammasome Substrates

We next wondered whether the unconventional process described above islimited to inflammasome substrates epitomized by IL-1 that areconcomitantly with their secretion proteolytically processed fromprecursor pro-proteins into mature forms. We tested whether induction ofautophagy affected other proteins not connected to proteolytic processsing in the inflammasome, such as HMGB1 (high mobility group box 1protein). HMGB1 is a major proinflammatory alarmin or DAMP(damage-associated molecular pattern) normally present in the nucleus(Andersson and Tracey, 2011). This chromatin-associated nuclear protein(with additional intracellular and extracellular signalling roles), uponexposure to inputs including those that induce autophagy (Singh et al,2010; Tang et al, 2010), undergoes a complex set of biochemical andlocalization changes. In the process, it first translocates from thenucleus into the cytoplasm and then is released from the cytoplasm toact in tissue remodeling signalling (when acting alone) or as aninflammatory mediator (when combined with bacterial agonists or otheralarmins such as IL-1 f:1). When tested, starvation and nigericinco-treatment caused HMGB1 extracellular release in an Atg5-dependentmanner (FIG. 6AX3). HMGB1 band was detected by immunoblots in BMMsculture supernatants upon stimulation of cells with nigericin, whereasHMGB1 was largely diminished when BMMs from Atg5fl/fl Cre-LyzM mice weretested (FIG. 6BX3). Nigericin was used in these experiments as aninflammasome agonist based on the reports that HMGB1, along withadditional unconventional substrates, depends on inflammasome forsecretion although the protein itself is not subjected to proteolyticprocessing by caspase 1 (Keller et al, 2008; Willingham et al, 2009;Lamkanfi et al, 2010; Lamkanfi, 2011). These experiments show thatautophagy-based unconventional secretion affects release of HMGB1 in amanner similar to IL-1f:I. Our findings broaden the spectrum ofautophagy-based unconventional secretion substrates, and establish thistype of unconventional secretion as a more general process inextracellular delivery of cytosolic proteins.

Discussion

The data presented in this work outline several elements of theautophagy-based unconventional secretory pathway in mammalian cells.This type of unconventional secretion is shown here to support theextracellular delivery of inflammasome substrates, in particular, IL-1f3and IL-18 and may potentially have a broader number of clients. Arelevant aspect of the process described here is that induction ofautophagy is required to observe the manifestations of this type ofunconventional secretion. Since basal autophagy suppresses spuriousinduction of inflammasome (Nakahira et al, 2010; Zhou et al, 2011),autophagy provides both avoidance of unscheduled inflammasome activationand a platform for extracellular delivery of inflammasome substrates.Since a number of hormones, cytokines, pathogenassociated molecularpatterns, and danger-associated molecular patterns (Tang et al, 2010;Deretic, 2011) are known to induce or inhibit autophagy, a link betweenautophagy and secretion of major immunomodulatory cytokines such asIL-1f3 could significantly influence the extent and duration ofinflammation. Connections between metabolic syndrome, high fat diet, andinflammasome activity are now beginning to be appreciated (Vandanmagsaret al, 2011; Wen et al, 2011), and we propose that autophagy-basedunconventional secretion may be a key coupler between the metabolism andinflammation.

Since a number of genetic links have been found between autophagy andidiopathic inflammatory diseases or infectious diseases with significantinflammatory components (Levine et al, 2011), it is possible that atleast in part the genetic associations between autophagy risk loci anddisease states may stem from altered autophagy-based unconventionalsecretion of inflammatory cytokines. The role of autophagy wasrepresented here by the effects of induction of autophagy and byemploying conditional knockout mice with a loss of Atg5 in macrophages.We interpret the incomplete inhibition of IL-1β secretion uponere-dependent Atg⁵⁰fl/fl excision as a result of the composite effectsof Atg5-dependent basal autophagy (inhibitory) (Zhou et al, 2011) andinduced autophagy (stimulatory) although we cannot exclude thepossibility of slight leakiness of the Atg⁵fl/fl LyzM-Cre system or theexistence of additional pathways. Importantly, blocking autophagicmaturation has not salvaged IL-1p but rather inhibited its secretion.This appears to be in contrast to what has been reported for Acb1 inyeast (Manjithaya et al, 2010). Moreover, cathepsin B activity wasneeded, suggesting that autophagic organelles here did not function asmere cargo carriers but provided a platform for activation ofinflammasome and IL-1b. In keeping with these observations, cathepsin Bhas been implicated in inflammasome activation in response toparticulate inflammasome agonists (Halle et al, 2008; Hornung et al,2008), such as those (alum, amyloid-b) used here in addition tonigericin, but how the substrate and cathepsin B meet has hitherto notbeen defined. Our data indicate that induction of autophagy enhancesassembly of inflammasome-activating components and suggest thatautophagic organelles may be a platform for concentration of componentsengaged in proteolytic activation of inflammasome components andinflammasome substrates. In keeping with this model of a muster stationfor inflammasome components, activation and subsequent extracellulardelivery, is the translocation of pro-IL-1 P to membranous organellesupon stimulation with the inflammasome agonist nigericin, as previouslyobserved by Sitia and colleagues (Rubartelli et al, 1990) who haveestablished early on that this process does not follow the conventionalsecretory pathway. The autophagy-based unconventional secretion pathwayin mammalian cells includes GRASP, one of the peripheral Golgi proteinsinvolved in lateral organization of Golgi ribbons. Although the role ofGRASP in alternative secretory pathway has been studied, its exactmechanism of action has not been elucidated (Kinseth et al, 2007; Nickeland Rabouille, 2009). We observed here a potentially telling connectionbetween GRASP and autophagy, by showing that GRASP affects autophagyinduction, which places GRASP upstream of autophagy execution, includingthe conjugation systems involved in LC3 lipidation. The response ofGRASP to nigericin stimulation in terms of its redistribution andjuxtaposition to autophagic organelles further links autophagy,inflammasome, and GRASP, although alternative explanations are possible.The finding that Rab8a plays a functional role in autophagy-basedunconventional secretion is of significance not just by assigning atrafficking regulator to this pathway but also by providing additionallinks with exocyst components, implicated to cooperate with Rab8a inother systems (Mazelova et al, 2009; Bryant et al, 2010) and to play arole in autophagy (Bodemann et al, 2011).

In summary, in this study we have uncovered the role of autophagy in thesecretion of cytosolic proinflammatory factors that cannot enter theconventional biosynthetic pathway due to the absence of leader peptidesthat would bring them into the ER and the organelles of the canonicalsecretory pathway. Both cytosolic IL-1p and IL-18 are processed fromtheir precursor proteins into their active forms via the inflammasomeapparatus (Davis et al, 2011; Lamkanfi, 2011); however, the process thatdelivers the proteolytically activated IL-1p and IL-18 to theextracellular environment has hitherto remained unclear. To be eligiblefor export outside of the cell without invoking a pore mechanism,cytosolic proteins first need to be brought somehow into the lumen ofvesicular carriers, as previously shown by others (Rubartelli et al,1990). We have elsewhere noted (Deretic, 2005, 2011) that autophagy is abulk topological inverter for cytosolic proteins and other molecules,ferrying them from the cytosol into the organellar lumen. We now showthat induction of autophagy does that with IL-1p in the process of itssecretion. In doing so, autophagic machinery cooperates with the Golgiassociated factor GRASP and post-Golgi membrane trafficking andexocytosis regulator Rab8a. Autophagy captures cytosolic IL-1p andbrings IL-1p into the organelles of a specialized unconventionalsecretory pathway. Broadening the scope of autophagy-based alternativesecretion pathway is the observation that it facilitates exit from cellsof the alarmin HMGB1. HMGB1 is a DAMP that is actively released fromimmune cells unlike its passive release from several cell typessecondary to cell death (Andersson and Tracey, 2011). It has beenrecently shown that inflammasome, rather unexpectedly given that HMGB1is not a known substrate for caspase-1 processing, plays a role in HMGB1release (Lamkanfi et al, 2010). One explanation that can be offeredbased on our studies is that a role of inflammasome may not be relatedsolely to proteolytic substrate processing but that it may be hardwiredinto the secretory pathway studied here. This is in keeping with therequirement for NLRP3 and ASC and not the caspase 1 activity for HMGB1release as a recently recognized non-canonical inflammasome client(Willingham et al, 2009). We propose here that autophagy-basedunconventional secretion may be used for extracellular delivery of aspectrum of cytosolic proteins or processed cytoplasmic substrates, notrestricted to the proteins explored here, and possibly including otherbiological mediators such as the recently discovered cryptides (Deretic,2005; Ponpuak et al, 2010). A recent study that appeared while this workwas in revision suggests that an unconventional secretion process, alsodependent on GRASP and autophagic machinery, may facilitate plasmamembrane delivery of mutant CFTR, potentially expanding the range ofsubstrates to integral membrane proteins (Gee et al, 2011). Given thecapacity for either bulk transport or selectivity when coupled withautophagic adaptors, we predict that autophagy-based unconventionalsecretion serves a potentially broad spectrum of yet to be uncoveredphysiological functions.

Materials and Methods Macrophages

Murine BMM cells were prepared from femurs of C57/BL6 mice, Atg⁵fl/flLyzM-Cre mice (Zhao et al, 2008) and their Cre-negative Atg5fl/fllittermates, and GFP-LC3 transgene knock-in mice (Mizushima et al, 2004)as previously described (Ponpuak et al, 2010). RAW 264.7 macrophageswere maintained and manipulated as previously described (Ponpuak et al,2010).

Pharmacological Agonists, Inhibitors, Injlammasome, and Autophagy

To induce pro-IL-1 p expression, cells were pretreated overnight with100 ng/ml LPS (Sigma). Inflammasome was induced with 20 mM nigericin(Sigma) for 1 h or with 250 mg/ml Alum (Thermoscientific) for 1 h orwith 250 mg/ml silica crystals (MIN-U-SIL-15, US Silica) for 1 h or with5 mM Amyloid-b peptide (Ab; American Peptide Company) fibrils preparedas described (Moore et al, 2002). Cells were treated with 100 nMbafilomycin A1 (LC Laboratories) or 10 mM cathepsin B inhibitor (CA-074Me) (Enzo Life Science). Autophagy was induced for 1 h by starvation inEBSS or with pp242 in full medium (Torkinib; Chemidea). Starvation andother treatments (except for macrophage priming with LPS done inadvance) were carried out concurrently (i.e., initiated at the sametime).Transfections and siRNA KnockdownsBMM and RAW 264.7 cells were transfected by nucleoporation usingNucleofector Reagent Kit V or Kit Mouse Macrophage (Amaxa/LonzaBiosystems). For murine NLRP3, ASC, Rab8a or GRASP knockdowns, cellswere transfected with siGENOME SMARTpool reagents (Dharmacon). Rab8aSMARTpool (GAAUAAG UGUGAUGUGAAU; GAAGACCUGUGUCCUGUUC; GACCUACGAUUACCUGUUC; GAGCAGCCAUGGAGUCAAG), ASC SMARTpool (AUACAUCCCUACUUGGUGA;GCUUAGAGACAUGGGCUUA; GCAACUGCGAGAAGGCUAU; CUGCAAACGACUAAAGAAG), NLRP3SMARTpool (GUUCUUCGCUGCUAUGUAC; GCACCCAGGCUGUAACAUU; UGAAGGACCCACAGUGUAA; UCACAUUCCUCUAUGGUAU), GORASP1 SMARTpool(CAUGAAGGUGCGCGAGGUA; CAGAGGACAUUGGU UCUAG; ACUCGAGGCUGAACAAGGA;GCUACGACCUCACAACUUA), and GORASP2 SMARTpool (GAAGACCUGUUCAGCCUUA;UACCAAGUCUGAUGCCUUU; GUAAACCAGUCCCUUGCUU; GAUCAUCACACCAAACUCU).Non-targeting siRNA pool (Scrambled) was used as a control. Plasmidencoding tandem RFP-GFP-LC3 fusion for quantification of autophagicmaturation was from T Yoshimori (Osaka, Japan). Plasmids encoding Rab8awt (wild type) and Rab8a S22N were from Johan Peranen (University ofHelsinki, Finland).

Antibodies, Immunoblotting, Detection Assays, and Microscopy

Cells extracts were analysed by standard immunoblot techniques withantibodies to pro-IL-I P (Abeam), NLRP3 (AdipoGen), ASC (Enzo LifeSciences), LC3 (Sigma), GRASP65 (Novus), GRASP55 (Abeam), Rab8a (Abeam),and Actin (Sigma); staining was revealed with Super Signal West Durachemiluminescent substrate (Pierce). For all conditions, cell-freesupernatants were assayed by immunoblotting after TCA precipitation formouse IL-I P pl 7 (R&D), caspase-1 p10 (Santa Cruz Biotechnology), HMGB1(Abeam) and Cathepsin B (R&D) or by ELISA for mouse IL-1p (R&D), IL-18(MBL), and HMGB1 (IBL). Immunofluorescence confocal microscopy wascarried out using a Zeiss LSM 510 Meta microscope (laser wavelengths488, 543, and 633 nm). Antibodies against endogenous proteins IL-IP(Abeam), Sec6 (Shu C Hsu, Rutgers University, NJ, USA), Cathepsin B(R&D), Rab8a (Abeam), GORASP1 (Novus), GORASP2 (ProteinTech Group),GM130 (BD), LC3 (MBL) and GFP (Abeam; for BMMs from GFP-LC3 knock-intransgenic mice) were used for indirect immunofluorescence analysis.Pearson's colocalization coefficients were derived using SLIDEBOOK 5.0(Intelligent Imaging Innovations) applying the SLIDEBOOK 5 defaultalgorithm command ‘AND’. All Pearson's coefficients were derived fromthree completely independent experiments with five fields or more perexperiment, for a total of ×15 fields contributing to the cumulativeresult.

Statistics

All data were analysed using two-tailed unpaired Student's t-tests. Allexperiments were performed at least three times, with data representingmean values±s.d. (standard deviation).

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Example 4 LC3B-II Autophagy Marker can be Detected on the Surface ofCells

Counterintuitively, given the engagement of autophagy and intracellularmembranes, we tested whether an autophagy marker can be detected on thesurface of cells. We find surprisingly that LC3B-II (which has beenfound only on intracellular membranes detectable by complicated methodsof microscopy) is detected by simple antibody staining on the cellsurface of primary lymphocytes using antibodies and flow cytometry orother simple assays of detection (FIG. 1X4). Based on prior art aboutautophagy one could not predict that LC3B would be exposed on thesurface of the plasma membrane (Scheme 1, PM) of the cell, such as ablood lymphocyte. This is due to the accepted topology of the LC3distribution on the intracellular membranes. Even if the intracellularmembranes were to fuse with the plasma membrane (PM), LC3 would not beexposed to the outside (see Scheme 1, conventional process A; accordingto the current knowledge LC3 would always be shielded from the exposureto the outside and not accessible to antibodies, unless the cells werepermeabilized). Scheme 1 process B, depicts what we experimentallydetect, i.e. LC3 is exposed on the cell surface on the side of theplasma membrane facing the outside of the cell and thus being accessibleto the exogenously added antibody to recognize LC3.

The first application of this finding is that, as shown in FIG. 1X4,blood from patients or subjects can be drawn, and white blood cells (ormore specifically different cell populations including CD4 and CDS cellsand their subsets) untreated or exposed to starvation in a buffer(simple PBS or EBSS) for a period of time (FIG. 1X4 is 90 min in EBSS)and LC3 detected on the surface by antibody staining withoutspecifically permeabilizing the cells. This new principle is the basisfor the following: (i) clinical tests for patients (blood drawing andstaining for LC3 on lymphocytes or whole white blood cells), (b)biomarker in clinical studies (same as above), (iii) drug screening anddevelopment for induction or blocking of autophagy, and (iv) target fortreatment with blocking antibodies should LC3 on the cell surface showbiological functions.

Example 5 Use of High-Content Imaging to Determine Autophagy-AssociatedEffects on Cytoplasmic Puncta

The experiment of this example showed that high-content imaging can beused in a high-throughput format to determine autophagy-associatedeffects on cytoplasmic puncta of M tuberculosis-infected lung cells andcells implicated in a lipid-related metabolic disorder.

Our high-content imaging system is represented schematically in FIG. 3X5and can be used to screen for a composition's autophagy-associatedeffect on cytoplasmic puncta of either M tuberculosis-infected lungcells or cells implicated in a lipid-related metabolic disorder. Thefollowing steps were performed:

(a) culturing a sample of the cells; (b) plating the cell sample onmulti-well plates;(c) contacting the cell sample with the composition; and (d) usinghigh-content imaging to examine the cell sample for anautophagy-associated effect on cytoplasmic puncta. The screen wasconducted using a high-throughput format.

More specifically, the multi-well plates were 384-well plates, the cellswere transfected with RFP-LC3 or GFP-LC3 prior to plating, and theobserved cytoplasmic puncta were RFP-LC3 puncta or GFP-LC3 puncta. SeeFIGS. 2X5, 3X5, 4X5. Positive controls and read times are summarized inFIG. 5AX5.

Red puncta and green puncta number, intensity, and area were consideredas selection parameters. FIG. 6X5. Screens using compounds from thePrestwick library were conducted and total GFP+ puncta area/cell andtoal GFP area/cell were determined. FIG. 7X5. An approximately 34%overlap of hits from two separate Prestwick screens from induction ofautophagy was observed. Compound hits, both real and imagined, weredetermined, FIG. 9X5, and dose response curve to pp242 were generated.FIG. 10X5. Comparable TPIMS screen results are summarized in FIG. 11X5.

Example 6

A number of compounds have been identified by screening small moleculelibraries for their autophagic regulatory capacities by using aCellomics ArrayScan to quantitate LC3-GFP/RFP puncta in HeLa cells. LC3is a widely-used marker for autophagic vacuoles. HeLa cells stablytransduced with LC3-GFP/RFP tandem construct generate fluorescentautophagic puncta, which are either green/yellow (early autophagosomes)or red (late autophagosomes fused with lysosomes, which degrades theGFP). By quantitating the number or total area of fluorescent puncta percell, we can detect alterations in autophagic flux and regulation.

Prior to any actual screening, however, preliminary experiments tomodify our protocols for use in 384-well plate high-content screeninghad to be conducted. To that end, we ran a series of experiments to showthat −5,000 LC3-GFP/RFP HeLa cells per well of a 384-well plate wasoptimal for imaging on the Cellomics ArrayScan. The next question waswhich parameter was most sensitive for detecting changes in autophagy.We tested total puncta area, number, or intensity per cell for both GFP+and RFP+ puncta after treatment with pp242, an mTOR inhibitor and knowninducer of autophagy. As shown in FIG. 1X6, GFP+ puncta area was themost distinct readout for induction of autophagy, although otherparameters in both the RFP and GFP channels also showed changes. Othermethods of induction of autophagy were tested for use as positivecontrols, including starvation and the mTOR inhibitor rapamycin (datanot shown). However, pp242 was consistently the stronger inducer ofautophagy in our hands in this assay, and was used in most studies.

Using the above system, we performed two separate screens on a chemicallibrary. This library contains 1,200 FDA-approved compounds, andrepresents wide functional and chemical diversity. This library spansfour 384-well plates, with 64 wells on each plate with DMSO only asnegative controls. We used 32 of these wells for addition of ourpositive control (pp242 or rapamycin), and left the other 32 for DMSOnegative controls. FIG. 2X6 shows the raw data from one of thesescreens. The first screen revealed 266 “hits”—compounds that induced ordecreased autophagy in the LC3-GFP/RFP HeLa cells. A hit was defined as3 standard deviations above or below the mean of the negative controlwells on a given plate. The second screen gave 182 hits. Overall, 96compounds were found to affect autophagy in both screens, for an overlaprate of −34% (FIG. 3X6). Analysis of the images from the experimentsrevealed that 6 of these compounds were false positives (due toautofluorescence, etc). Therefore, a total of 90 compounds wereidentified from the two chemical library screens and appear in thepresent specification.

In order to further dissect the ability of the 90 hits to affectautophagy, we wished to test whether the screening system we used wassufficient to determine dose responses for each compound. To that end,we performed dose response experiments using pp242. As shown in FIG. 4,dose responses could be performed successfully.Therefore, we performed two separate dose response experiments on 85 ofthe 90 hits obtained from the two Prestwick Chemical Library screens. Asshown in Appendix 2, a range of dose response curves were identified inthe different compounds. This assay resulted in 25 compounds that showedacceptable dose response curves in both experiments; 20 of thesecompounds were not previously known to induce autophagy. Current studiesare underway to measure LC3-I and LC3-II levels by western blot, and p62levels by Cellomics and western blot, to further confirm the autophagicactivity of these compounds.In parallel to the second Prestwick Chemical Library screen, we alsowished to test which compounds might be useful for combinatorial drugproducts. Using the data from FIG. 4, we treated LC3-GFP/RFP HeLa cellswith a suboptimal dose of pp242 that did not induce autophagy (−0.06uM), then added the Prestwick Chemical Library to these cells andanalyzed as before. After two separate screens, we found 8 compounds(Appendix 4) that altered autophagy in the presence, but not theabsence, of suboptimal pp242 concentration. Four of these 8 compoundswere found in either of our prior Prestwick Chemical Library screen orare known mTOR pathway modulators (and therefore merely exertingadditive effects). Therefore, 4 compounds in this screen could modulateautophagy in concert with, but not without, suboptimal amounts of pp242.We are currently testing these compounds in dose response experiments toconfirm the pp242 effects and to test whether any activity is additiveor synergistic.Wild-type HIV-1 viruses will be used in further tests to determinewhether the compounds in our screens will alter HIV-1 replication. Wehave already grown and titered a wild-type macrophage-tropic HIV-1. Twoseparate wild-type CD4+ T cell-tropic HIV strains have also beengenerated. Compounds that inhibit or induce autophagy, as identified inour ongoing screens, will be incubated with human peripheral bloodmonocyte-derived macrophages that have been infected with wild-typeHIV-1 in 96-well plates. At different time points, supernatants will beharvested and added to TMZ-bl/JC53BL cells, which express luciferaseafter HIV replication. Replication will be assessed by luciferase levelsrelative to DMSO-treated controls. Alternately, p24 levels will beassessed.We have also performed two separate screens using the LC3-GFP/RFP HeLacells against the Spectrum 2000 library. As shown in FIG. 5, 207compounds were identified as regulators of autophagy. After visualinspection of the images, 21 compounds were excluded due toautofluorescence or other false positive characteristics. Of theremaining 186 compounds, 94 were also present in the Prestwick ChemicalLibrary, so these were excluded. This left 92 compounds, 83 of whichwere not known to be regulators of autophagy. There is a range ofcompound types in this group (FIG. 5). These compounds have beendescribed in the specification as set forth above.

Summary

We have optimized our high-content imaging screening system formeasurement of regulation of autophagy. We have used this system toscreen two different drug libraries and have identified up to 182compounds (125 of which have been used in humans) that regulateautophagy, and have conducted dose response studies to begin to narrowdown these hits to identify the most promising compounds. In addition,we have found 4 compounds that only induce autophagy in a combinationsetting (with low doses of pp242). We are in the process of setting upour HIV in vitro replication assay to further test these hits.Additional library screens are planned.

1-85. (canceled)
 86. A pharmaceutical composition for use in thetreatment of tuberculosis comprising: (a) an effective amount of atleast one compound as an autophagy modulator selected from the groupconsisting of rapamycin, flubendazole, bromhexine and curcumin; and (b)an effective amount of an anti-tuberculosis agent, further incombination with a pharmaceutically-acceptable carrier, additive and/orexcipient.
 87. The composition according to claim 86 wherein saidcompound is rapamycin, flubendazole, bromhexine or a mixture thereof.88. The composition according to claim 86 wherein said compound israpamycin, bromhexine, curcumin or a mixture thereof.
 89. Thecomposition according to claim 86 wherein said compound is rapamycin,flubendazole, curcumin or a mixture thereof.
 90. The compositionaccording to claim 86 wherein said compound is flubendazole, bromhexin,curcumin or a mixture thereof.
 91. The composition according to claim 86wherein said compound is flubendazole, rapamycin or a mixture offlubendazole and rapamycin.
 92. The composition according to claim 86wherein said compound is rapamycin, curcumin or a mixture of rapamycinand curcumin.
 93. The composition according to claim 86 wherein saidautophagy modulator comprises rapamycin, brombexine or a mixture ofrapamycin and bromhexine.
 94. The composition according to claim 86wherein said autophagy modulator comprises rapamycin, brombexine,curcumin or a mixture thereof.
 95. The composition according to claim 86wherein said autophagy modulator comprises rapamycin, flubendazole andbrombexine.
 96. The composition according to claim 86 wherein saidautophagy modulator comprises flubendazole, rapamycin and curcumin. 97.The composition according to claim 85 comprising flubendazole,bromhexine, rapamycin and curcumin.
 98. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 86. 99. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 87. 100. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 88. 101. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 89. 102. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 90. 103. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 91. 104. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim
 92. 105. A method of treatingtuberculosis in a patient in need comprising administering to saidpatient a composition according to claim 93.